From cea652244ddca6f80710af752762604f1cb67165 Mon Sep 17 00:00:00 2001 From: Bonny Jain Date: Sat, 18 May 2013 00:22:30 -0400 Subject: [PATCH] Raw data and synthetic network source files from Purcell et al. 2013 --- data/GFPOptimizedTimeData.mat | Bin 0 -> 1191 bytes data/GFPRNAData.mat | Bin 0 -> 1531 bytes data/GFPTimeData.mat | Bin 0 -> 1219 bytes data/NoGeneRNAData.mat | Bin 0 -> 1543 bytes data/NoGeneTimeData.mat | Bin 0 -> 1187 bytes data/araCOptimizedTimeData.mat | Bin 0 -> 1179 bytes data/araCRNAData.mat | Bin 0 -> 1512 bytes data/araCTimeData.mat | Bin 0 -> 1207 bytes data/lacIOptimizedTimeData.mat | Bin 0 -> 1213 bytes data/lacIRNAData.mat | Bin 0 -> 1527 bytes data/lacITimeData.mat | Bin 0 -> 1208 bytes data/tetROptimizedTimeData.mat | Bin 0 -> 1218 bytes data/tetRRNAData.mat | Bin 0 -> 1523 bytes data/tetRTimeData.mat | Bin 0 -> 1207 bytes .../+covert/+cell/+sim/+runners/NoGene1.m | 33 + .../+covert/+cell/+sim/+runners/NoGene10.m | 33 + .../+covert/+cell/+sim/+runners/NoGene100.m | 33 + .../+covert/+cell/+sim/+runners/NoGene20.m | 33 + .../+covert/+cell/+sim/+runners/NoGene5.m | 33 + .../+covert/+cell/+sim/+runners/NoGene50.m | 34 + .../+sim/+runners/SimulationRunnerDecay1.m | 563 ++++ .../+covert/+cell/+sim/+runners/SingleGFP1.m | 75 + .../+covert/+cell/+sim/+runners/SingleGFP10.m | 291 ++ .../+cell/+sim/+runners/SingleGFP100.m | 2451 +++++++++++++++++ .../+covert/+cell/+sim/+runners/SingleGFP20.m | 531 ++++ .../+covert/+cell/+sim/+runners/SingleGFP5.m | 171 ++ .../+covert/+cell/+sim/+runners/SingleGFP50.m | 1251 +++++++++ .../+cell/+sim/+runners/SingleGFPOptimized1.m | 75 + .../+sim/+runners/SingleGFPOptimized10.m | 291 ++ .../+sim/+runners/SingleGFPOptimized100.m | 2451 +++++++++++++++++ .../+sim/+runners/SingleGFPOptimized20.m | 531 ++++ .../+cell/+sim/+runners/SingleGFPOptimized5.m | 171 ++ .../+sim/+runners/SingleGFPOptimized50.m | 1251 +++++++++ .../+covert/+cell/+sim/+runners/SinglearaC1.m | 75 + .../+cell/+sim/+runners/SinglearaC10.m | 291 ++ .../+cell/+sim/+runners/SinglearaC100.m | 2451 +++++++++++++++++ .../+cell/+sim/+runners/SinglearaC20.m | 531 ++++ .../+covert/+cell/+sim/+runners/SinglearaC5.m | 171 ++ .../+cell/+sim/+runners/SinglearaC50.m | 1251 +++++++++ .../+sim/+runners/SinglearaCOptimized1.m | 75 + .../+sim/+runners/SinglearaCOptimized10.m | 291 ++ .../+sim/+runners/SinglearaCOptimized100.m | 2451 +++++++++++++++++ .../+sim/+runners/SinglearaCOptimized20.m | 531 ++++ .../+sim/+runners/SinglearaCOptimized5.m | 171 ++ .../+sim/+runners/SinglearaCOptimized50.m | 1251 +++++++++ .../+covert/+cell/+sim/+runners/SinglelacI1.m | 120 + .../+cell/+sim/+runners/SinglelacI10.m | 482 ++++ .../+cell/+sim/+runners/SinglelacI100.m | 2451 +++++++++++++++++ .../+cell/+sim/+runners/SinglelacI20.m | 531 ++++ .../+covert/+cell/+sim/+runners/SinglelacI5.m | 280 ++ .../+cell/+sim/+runners/SinglelacI50.m | 1251 +++++++++ .../+sim/+runners/SinglelacIOptimized1.m | 120 + .../+sim/+runners/SinglelacIOptimized10.m | 482 ++++ .../+sim/+runners/SinglelacIOptimized100.m | 2451 +++++++++++++++++ .../+sim/+runners/SinglelacIOptimized20.m | 531 ++++ .../+sim/+runners/SinglelacIOptimized5.m | 280 ++ .../+sim/+runners/SinglelacIOptimized50.m | 1251 +++++++++ .../+covert/+cell/+sim/+runners/SingletetR1.m | 75 + .../+cell/+sim/+runners/SingletetR10.m | 291 ++ .../+cell/+sim/+runners/SingletetR100.m | 2451 +++++++++++++++++ .../+cell/+sim/+runners/SingletetR20.m | 531 ++++ .../+covert/+cell/+sim/+runners/SingletetR5.m | 171 ++ .../+cell/+sim/+runners/SingletetR50.m | 1251 +++++++++ .../+sim/+runners/SingletetROptimized1.m | 75 + .../+sim/+runners/SingletetROptimized10.m | 291 ++ .../+sim/+runners/SingletetROptimized100.m | 2451 +++++++++++++++++ .../+sim/+runners/SingletetROptimized20.m | 531 ++++ .../+sim/+runners/SingletetROptimized5.m | 171 ++ .../+sim/+runners/SingletetROptimized50.m | 1251 +++++++++ 69 files changed, 39612 insertions(+) create mode 100644 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function this = NoGene1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene10.m new file mode 100644 index 0000000..02af9be --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene10.m @@ -0,0 +1,33 @@ +classdef NoGene10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = NoGene10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene100.m new file mode 100644 index 0000000..3129d70 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene100.m @@ -0,0 +1,33 @@ +classdef NoGene100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = NoGene100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene20.m new file mode 100644 index 0000000..2c1660f --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene20.m @@ -0,0 +1,33 @@ +classdef NoGene20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = NoGene20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene5.m new file mode 100644 index 0000000..3f0ac83 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene5.m @@ -0,0 +1,33 @@ +classdef NoGene5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = NoGene5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene50.m new file mode 100644 index 0000000..91d3386 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene50.m @@ -0,0 +1,34 @@ +classdef NoGene50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = NoGene50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end + function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SimulationRunnerDecay1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SimulationRunnerDecay1.m new file mode 100644 index 0000000..ee01046 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SimulationRunnerDecay1.m @@ -0,0 +1,563 @@ +% Instantiate simulation from knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SimulationRunnerDecay1 < handle + %default options + properties (SetAccess = protected) + kbCache = 'data/knowledgeBase.mat' + simCache = 'data/Simulation_fitted%s.mat' + simJsonCache = 'data/%s.json' + + outDir = '' + logToDisk = false + logToDb = false + childDirs = {} + + useCachedKb = true + useCachedSim = true + cacheKb = false + cacheSimulation = false + end + + properties (Constant = true) + DEFAULT_DISPLACED_BY = { + 'DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE' + 'DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX' + 'DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE' + 'MG_001_DIMER' + 'MG_001_MONOMER' + 'MG_073_206_421_TETRAMER' + 'MG_094_HEXAMER' + 'MG_097_MONOMER' + 'MG_105_OCTAMER' + 'MG_184_DIMER' + 'MG_235_MONOMER' + 'MG_244_DIMER' + 'MG_254_MONOMER' + 'MG_262_MONOMER' + 'MG_339_MONOMER' + 'MG_352_DIMER' + 'MG_358_359_10MER' + 'MG_438_MONOMER' + 'MG_498_MONOMER' + 'RNA_POLYMERASE_HOLOENZYME' + 'RNA_POLYMERASE' + }; + DEFAULT_DISPLACES = { + 'DNA_GYRASE' + 'MG_122_MONOMER' + 'MG_203_204_TETRAMER' + 'MG_213_214_298_6MER_ADP' + 'MG_469_1MER_ADP' + 'MG_469_1MER_ATP' + }; + end + + methods + function this = SimulationRunnerDecay1(varargin) + if nargin >=1 && isstruct(varargin{1}) + options = varargin{1}; + else + options = struct(); + for i = 1:2:numel(varargin) + options.(varargin{i}) = varargin{i+1}; + end + end + + if isfield(options, 'childDir1') && isfield(options, 'childDir2') + options.childDirs = {options.childDir1; options.childDir2}; + end + + metaClass = metaclass(this); + for i = 1:numel(metaClass.Properties) + if isfield(options, metaClass.Properties{i}.Name) + this.(metaClass.Properties{i}.Name) = options.(metaClass.Properties{i}.Name); + end + end + end + + function [sim, kb] = run(this) + metaClass = metaclass(this); + simName = strrep(metaClass.Name, 'edu.stanford.covert.cell.sim.runners.', ''); + + %construct KB and simulation + fprintf('Constructing %s simulation ...\n', simName); + [sim, kb] = this.constructKbAndSimulation(); + + %run simulation + fprintf('Running %s simulation ...\n', simName); + this.runSimulation(sim); + end + + function [sim, kb] = constructKbAndSimulation(this) + import edu.stanford.covert.cell.sim.Simulation; + import edu.stanford.covert.cell.sim.util.FitConstants; + + %% load default KB and simulation + %load default network structure and parameters + [kb, kbWid] = this.loadDefaultNetwork(); + + %initialize simulation from default KB + defSim = this.loadDefaultSimulation(kb, kbWid); + + %% modify network + if isequal('edu.stanford.covert.cell.sim.runners.SimulationRunnerDecay1', class(this)) + sim = defSim; + else + %% modify structure + this.modifyNetworkStructure(kb); + + %% create simulation with modified structure + modSim = Simulation(kb.states, kb.processes); + modSim.initializeConstants(kb); + + %% merge fitted parameters into new simulation + defFitter = FitConstants(defSim, struct('verbosity', 1)); + modFitter = FitConstants(modSim, struct('verbosity', 1)); + + %get parameter values + defParams = defFitter.constructParameterVectorFromSimulation(); + modParams = modFitter.initializeFittedConstants(); + + [defRnaExp, defNmpComp, defAaComp, defRnaWtFracs, defRnaDecayRates, ... + defBioComp, defBioProd, defByprod, defUnaccECons] = ... + defFitter.extractParameterVector(defParams); + [modRnaExp, ~, ~, ~, modRnaDecayRates, ... + modBioComp, modBioProd, modByprod, ~] = ... + modFitter.extractParameterVector(modParams); + + %merge default parameter values into modified simulation + defMet = defSim.state('Metabolite'); + modMet = modSim.state('Metabolite'); + [tfs, idxs] = ismember(modMet.wholeCellModelIDs, defMet.wholeCellModelIDs); + modBioComp(tfs) = defBioComp(idxs(tfs)); + modBioProd(tfs) = defBioProd(idxs(tfs)); + modByprod(tfs) = defByprod(idxs(tfs)); + modBioComp(~tfs) = 0; + modBioProd(~tfs) = 0; + modByprod(~tfs) = 0; + + defRna = defSim.state('Rna'); + modRna = modSim.state('Rna'); + [tfs, idxs] = ismember(modRna.wholeCellModelIDs(modRna.matureIndexs), defRna.wholeCellModelIDs(defRna.matureIndexs)); + modRnaExp(tfs) = defRnaExp(idxs(tfs)); + modRnaDecayRates(tfs) = defRnaDecayRates(idxs(tfs)); + modRnaExp(~tfs) = 0; + + modNmpComp = defNmpComp; + modAaComp = defAaComp; + modRnaWtFracs = defRnaWtFracs; + modUnaccECons = defUnaccECons; + + %set parameters + modParams = modFitter.constructParameterVector(... + modRnaExp, modNmpComp, modAaComp, modRnaWtFracs, modRnaDecayRates, ... + modBioComp, modBioProd, modByprod, modUnaccECons); + modFitter.applyParameterVectorToSimulation(modParams); + + %% modify parameter values + this.modifyNetworkParameters(modSim); + + %% return new simulation + sim = modSim; + end + end + + function [val, growths] = isSimulationFitted(~, sim, nSample) + import xunit.utils.compareFloats; + if nargin < 3 + nSample = 100; + end + + %handle to MetabolicReaction state + mr = sim.state('MetabolicReaction'); + + %save filter + initialGrowthFilterWidth = mr.initialGrowthFilterWidth; + mr.initialGrowthFilterWidth = Inf; + + %sample initial conditions + growths = zeros(nSample, 1); + for i = 1:nSample + sim.applyOptions('seed', i); + sim.initializeState(); + growths(i) = mr.growth; + end + + %restore filter + mr.initialGrowthFilterWidth = initialGrowthFilterWidth; + + %test + val = ... + compareFloats(mr.meanInitialGrowthRate, mean(growths(growths > 1e-6)), 'elementwise', 'relative', 1e-1, sqrt(eps)) && ... + compareFloats(mr.meanInitialGrowthRate, median(growths(growths > 1e-6)), 'elementwise', 'relative', 1e-1, sqrt(eps)); + end + + % write simulation data + function cacheSimulationParametersJson(this, sim) + data = {'options', 'parameters', 'fixedConstants', 'fittedConstants'}; + for i = 1:numel(data) + fid = fopen(sprintf(this.simJsonCache, data{i}), 'w'); + tmp = sim.(['get' upper(data{i}(1)) data{i}(2:end)])(); + if ismember(data{i}, {'fixedConstants', 'fittedConstants'}) + for j = 1:numel(sim.states) + stateID = sim.states{j}.wholeCellModelID(7:end); + fields = fieldnames(tmp.states.(stateID)); + for k = 1:numel(fields) + tmp.states.(stateID).(fields{k}) = []; + end + end + + for j = 1:numel(sim.processes) + processID = sim.processes{j}.wholeCellModelID(9:end); + fields = fieldnames(tmp.processes.(processID)); + for k = 1:numel(fields) + tmp.processes.(processID).(fields{k}) = []; + end + end + end + fwrite(fid, edu.stanford.covert.io.jsonFormat(tmp)); + fclose(fid); + end + end + + %% write simulation test fixture + function cacheSimulationTestFixtures(~, sim) + %import + import edu.stanford.covert.cell.sim.CellStateFixture; + import edu.stanford.covert.cell.sim.ProcessFixture; + import edu.stanford.covert.cell.sim.SimulationFixture; + + %store simulation fixture + SimulationFixture.store(sim, 'Simulation.mat'); + + %% unset mass reference in geometry state to reduce fixture sizes + mass = sim.state('Mass'); + sim.state('Geometry').mass = []; + + %% write state test fixtures + for i = 1:length(sim.states) + CellStateFixture.store(sim.states{i}); + end + + %% write process test fixtures + for i = 1:length(sim.processes) + ProcessFixture.store(sim.processes{i}); + end + + %% reset mass reference in geometry state, and regenerate fixtures + sim.state('Geometry').mass = mass; + CellStateFixture.store(sim.state('Geometry')); + ProcessFixture.store(sim.process('Metabolism')); + end + + function runSimulation(this, sim) + %% import + import edu.stanford.covert.cell.sim.constant.Condition; + import edu.stanford.covert.cell.sim.util.ConditionSet; + import edu.stanford.covert.cell.sim.util.DatabaseLogger; + import edu.stanford.covert.cell.sim.util.DiskLogger; + import edu.stanford.covert.cell.sim.util.SummaryLogger; + import edu.stanford.covert.db.MySQLDatabase; + + %% process options, setup loggers + summaryLogger = SummaryLogger(1, 2); + loggers = {summaryLogger}; + ic = []; + + %load perturbations + if ~isempty(this.outDir) && exist([this.outDir filesep 'conditions.xml'], 'file') + data = ConditionSet.parseConditionSet(sim, [this.outDir filesep 'conditions.xml']); + data.metadata.knowledgeBaseWID = knowledgeBaseWID; + sim.applyOptions(data.options); + sim.applyOptions(data.perturbations); + sim.applyParameters(data.parameters); + summaryLogger.setOptions(struct('verbosity', sim.verbosity, 'outputDirectory', this.outDir)); + end + + %load initial conditions + if ~isempty(this.outDir) && exist([this.outDir filesep 'initialConditions.mat'], 'file') + ic = load([this.outDir filesep 'initialConditions.mat']); + end + + %setup disk logger + if this.logToDisk + diskLogger = DiskLogger(this.outDir, 100); + if exist('data', 'var') + diskLogger.addMetadata(data.metadata); + else + diskLogger.addMetadata(struct(... + 'shortDescription', '', ... + 'longDescription', '', ... + 'email', '', ... + 'firstName', '', ... + 'lastName', '', ... + 'affiliation', '', ... + 'knowledgeBaseWID', '', ... + 'revision', '', ... + 'differencesFromRevision', '', ... + 'userName', '', ... + 'hostName', '', ... + 'ipAddress', '' ... + )); + end + loggers = [loggers; {diskLogger}]; + end + + %setup database logger + if this.logToDb + databaseLogger = DatabaseLogger(MySQLDatabase(config), 1000); + databaseLogger.addMetadata(data.metadata); + loggers = [loggers; {databaseLogger}]; + end + + %% simulate + try + decayMultiplier = 50; + pm = sim.state('ProteinMonomer'); + matchA = strcmp(pm.wholeCellModelIDs, 'MonomerA'); + for i = 1:length(matchA) + if matchA(i) == 1 + pm.decayRates(i) = decayMultiplier * pm.decayRates(i); + end + end + pc = sim.state('ProteinComplex'); + matchAA = strcmp(pc.wholeCellModelIDs, 'ComplexAA'); + for i = 1:length(matchAA) + if matchAA(i) == 1 + pc.decayRates(i) = decayMultiplier * pc.decayRates(i); + end + end + + % cell cycle up to, but not including division + currentTime = clock; + newSeed = 10000 * (60 * currentTime(5) + currentTime(6)); + sim.applyOptions('seed', newSeed); + sim.run(ic, loggers); + + % division + if ~isempty(this.childDirs) && ... + sim.state('Chromosome').ploidy == 2 && ... + sim.state('Chromosome').segregated && ... + sim.state('Geometry').pinchedDiameter == 0 + [~, daughters] = sim.divideState(); + + daughter1 = daughters(1); %#ok + daughter2 = daughters(2); %#ok + + save([this.childDirs{1} filesep 'initialConditions.mat'], '-struct', 'daughter1'); + save([this.childDirs{2} filesep 'initialConditions.mat'], '-struct', 'daughter2'); + end + catch exception + if ~isempty(this.outDir) + errFile = ['tmp' filesep 'simulation_error_' datestr(now, 'yyyy_mm_dd_HH_MM_SS_FFF') '.mat']; + else + errFile = [this.outDir filesep 'err.mat']; + end + + try + save(errFile, 'sim'); + catch saveException + exception.addCause(MException('Simulation:runTimeError', ... + 'Simulation run-time error at %d. Unable to save simulation and exiting.', ... + sim.state('Time').values)).addCause(saveException).rethrow(); + end + + exception.addCause(MException('Simulation:runTimeError', ... + 'Simulation run-time error at %d. Saving simulation at ''%s'' and exiting.', ... + sim.state('Time').values, errFile)).rethrow(); + end + end + end + + methods (Access = protected) + function [knowledgeBase, knowledgeBaseWID] = loadDefaultNetwork(this) + import edu.stanford.covert.cell.kb.KnowledgeBase; + import edu.stanford.covert.cell.kb.KnowledgeBaseUtil; + import edu.stanford.covert.db.MySQLDatabase; + + if ~this.useCachedKb || ~exist(this.kbCache, 'file') + % connect to database + dbConnectionParameters = config(); + database = MySQLDatabase(dbConnectionParameters); + + % construct latest knowledge base from database + knowledgeBaseWID = KnowledgeBaseUtil.selectLatestKnowledgeBase(database); + knowledgeBase = KnowledgeBase(database, knowledgeBaseWID); + + %serialize + knowledgeBase.serializeLinks(); + + % save + if this.cacheKb + save(this.kbCache, 'knowledgeBase', 'knowledgeBaseWID'); + end + + %deserialize + knowledgeBase.deserializeLinks(); + + % cleanup + database.close(); + else + %load cached KB + tmp = load(this.kbCache); + knowledgeBase = tmp.knowledgeBase; + knowledgeBaseWID = tmp.knowledgeBaseWID; + knowledgeBase.deserializeLinks(); + end + end + + function sim = loadDefaultSimulation(this, kb, kbWid) + import edu.stanford.covert.cell.sim.Simulation; + import edu.stanford.covert.cell.sim.util.CachedSimulationObjectUtil; + import edu.stanford.covert.cell.sim.util.FitConstants; + + if ~this.useCachedKb || ~this.useCachedSim || ~exist(sprintf(this.simCache, ''), 'file') + sim = Simulation(kb.states, kb.processes); + sim.initializeConstants(kb); + sim.applyOptions('seed', 1); + + %fit simulation + fitter = FitConstants(sim, struct('verbosity', 1)); + fitter.run(); + + %choose an initial simulation state with desired growth rate + sim.applyOptions('seed', 1); + mr = sim.state('MetabolicReaction'); + initGrowthFilterW = mr.initialGrowthFilterWidth; + mr.initialGrowthFilterWidth = 1e-2; + sim.initializeState(); + mr.initialGrowthFilterWidth = initGrowthFilterW; + + %cache simulation object + if this.cacheSimulation + CachedSimulationObjectUtil.store(sim, kbWid, this.simCache); + end + else + sim = CachedSimulationObjectUtil.load(); + sim.constructRandStream(); + end + end + + function modifyNetworkStructure(~, kb) + kb.invalidate(); + kb.calcIndices(); + kb.computeDependentProperties(); + end + + function newRxns = createDefaultDisplacementReactions(this, kb, newProts) + import edu.stanford.covert.cell.kb.Reaction; + + cytosol = findobj(kb.compartments, 'wholeCellModelID', 'c'); + nucleoid = findobj(kb.compartments, 'wholeCellModelID', 'd'); + + chrState = findobj(kb.states, 'wholeCellModelID', 'State_Chromosome'); + + newRxns = Reaction.empty(0, 1); + for i = 1:numel(newProts) + for j = 1:numel(this.DEFAULT_DISPLACED_BY) + tmp = Reaction(kb, NaN, ... + {sprintf('DNABoundProteinRelease_%s_%s', this.DEFAULT_DISPLACED_BY{j}, newProts(i).wholeCellModelID)}, ... + {sprintf('DNA bound protein release (%s releases %s)', this.DEFAULT_DISPLACED_BY{j}, newProts(i).name)}, ... + {''}, {''}, {'N'}, {'F'}, NaN, NaN, ... + {''}, NaN, NaN, {'1/min'}, ... + {''}, NaN, NaN, {'1/min'}, ... + NaN, NaN, ... + {''}, {''}, ... + 0, 1000, {'mmol/gDCW/h'}); + newRxns = [newRxns; tmp]; %#ok + + tmp.state = chrState; + + tmpMon = findobj(kb.proteinMonomers, 'wholeCellModelID', this.DEFAULT_DISPLACED_BY{j}); + tmpCpx = findobj(kb.proteinComplexs, 'wholeCellModelID', this.DEFAULT_DISPLACED_BY{j}); + if ~isempty(tmpMon) + tmp.proteinMonomers = [tmpMon; tmpMon]; + tmp.proteinMonomerCompartments = [nucleoid; cytosol]; + tmp.proteinMonomerCoefficients = [1; -1]; + + tmp.proteinComplexs = [newProts(i); newProts(i)]; + tmp.proteinComplexCompartments = [cytosol; nucleoid]; + tmp.proteinComplexCoefficients = [1; -1]; + else + tmp.proteinComplexs = [newProts(i); newProts(i); tmpCpx; tmpCpx]; + tmp.proteinComplexCompartments = [cytosol; nucleoid; nucleoid; cytosol]; + tmp.proteinComplexCoefficients = [1; -1; 1; -1]; + end + end + + for j = 1:numel(this.DEFAULT_DISPLACES) + tmpMon = findobj(kb.proteinMonomers, 'wholeCellModelID', this.DEFAULT_DISPLACES{j}); + tmpCpx = findobj(kb.proteinComplexs, 'wholeCellModelID', this.DEFAULT_DISPLACES{j}); + if ~isempty(tmpMon) + tmp = Reaction(kb, NaN, ... + {sprintf('DNABoundProteinRelease_%s_%s', newProts(i).wholeCellModelID), tmpMon.wholeCellModelID}, ... + {sprintf('DNA bound protein release (%s releases %s)', newProts(i).name, tmpMon.name)}, ... + {''}, {''}, {'N'}, {'F'}, NaN, NaN, ... + {''}, NaN, NaN, {'1/min'}, ... + {''}, NaN, NaN, {'1/min'}, ... + NaN, NaN, ... + {''}, {''}, ... + 0, 1000, {'mmol/gDCW/h'}); + + if isa(newProts, 'edu.stanford.covert.cell.kb.ProteinMonomer') + tmp.proteinMonomers = [newProts(i); newProts(i); tmpMon; tmpMon]; + tmp.proteinMonomerCompartments = [cytosol; nucleoid; nucleoid; cytosol]; + tmp.proteinMonomerCoefficients = [-1; 1; -1; 1]; + else + tmp.proteinMonomers = [tmpMon; tmpMon]; + tmp.proteinMonomerCompartments = [nucleoid; cytosol]; + tmp.proteinMonomerCoefficients = [-1; 1]; + + tmp.proteinComplexs = [newProts(i); newProts(i)]; + tmp.proteinComplexCompartments = [cytosol; nucleoid]; + tmp.proteinComplexCoefficients = [-1; 1]; + end + else + tmp = Reaction(kb, NaN, ... + {sprintf('DNABoundProteinRelease_%s_%s', newProts(i).wholeCellModelID), tmpCpx.wholeCellModelID}, ... + {sprintf('DNA bound protein release (%s releases %s)', newProts(i).name, tmpCpx.name)}, ... + {''}, {''}, {'N'}, {'F'}, NaN, NaN, ... + {''}, NaN, NaN, {'1/min'}, ... + {''}, NaN, NaN, {'1/min'}, ... + NaN, NaN, ... + {''}, {''}, ... + 0, 1000, {'mmol/gDCW/h'}); + + if isa(newProts, 'edu.stanford.covert.cell.kb.ProteinMonomer') + tmp.proteinMonomers = [newProts(i); newProts(i)]; + tmp.proteinMonomerCompartments = [cytosol; nucleoid]; + tmp.proteinMonomerCoefficients = [-1; 1]; + + tmp.proteinComplexs = [tmpCpx; tmpCpx]; + tmp.proteinComplexCompartments = [nucleoid; cytosol]; + tmp.proteinComplexCoefficients = [-1; 1]; + else + tmp.proteinComplexs = [newProts(i); newProts(i); tmpCpx; tmpCpx]; + tmp.proteinComplexCompartments = [cytosol; nucleoid; nucleoid; cytosol]; + tmp.proteinComplexCoefficients = [-1; 1; -1; 1]; + end + end + + tmp.state = chrState; + + newRxns = [newRxns; tmp]; %#ok + end + end + + chrState.reactions = [chrState.reactions; newRxns]; + kb.reactions = [kb.reactions; newRxns]; + end + + function [rnaExp, nmpComp, aaComp, rnaWtFracs, rnaDecayRates, ... + bioComp, bioProd, byprod, unaccECons] = ... + modifyNetworkParameters(this, sim, ... + rnaExp, nmpComp, aaComp, rnaWtFracs, rnaDecayRates, ... + bioComp, bioProd, byprod, unaccECons) %#ok + end + end +end + + diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP1.m new file mode 100644 index 0000000..f0500b7 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP1.m @@ -0,0 +1,75 @@ +classdef SingleGFP1 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFP1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP10.m new file mode 100644 index 0000000..ca3e98f --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP10.m @@ -0,0 +1,291 @@ +classdef SingleGFP10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFP10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP100.m new file mode 100644 index 0000000..da1c4b4 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP100.m @@ -0,0 +1,2451 @@ +classdef SingleGFP100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFP100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 588347, 717, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 589164, 717, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 589981, 717, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 590798, 717, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 591615, 717, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 592432, 717, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 593249, 717, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 594066, 717, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 594883, 717, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 595700, 717, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 596517, 717, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 597334, 717, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 598151, 717, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 598968, 717, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 599785, 717, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 600602, 717, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 601419, 717, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 602236, 717, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 603053, 717, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 603870, 717, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 604687, 717, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 605504, 717, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 606321, 717, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 607138, 717, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 607955, 717, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 608772, 717, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 609589, 717, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 610406, 717, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 611223, 717, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 612040, 717, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 612857, 717, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 613674, 717, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 614491, 717, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 615308, 717, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 616125, 717, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 616942, 717, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 617759, 717, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 618576, 717, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 619393, 717, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 620210, 717, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 621027, 717, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 621844, 717, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 622661, 717, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 623478, 717, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 624295, 717, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 625112, 717, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 625929, 717, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 626746, 717, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 627563, 717, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 628380, 717, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 629197, 717, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 630014, 717, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 630831, 717, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 631648, 717, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 632465, 717, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 633282, 717, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 634099, 717, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 634916, 717, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 635733, 717, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 636550, 717, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 637367, 717, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 638184, 717, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 639001, 717, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 639818, 717, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 640635, 717, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 641452, 717, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 642269, 717, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 643086, 717, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 643903, 717, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 644720, 717, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 645537, 717, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 646354, 717, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 647171, 717, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 647988, 717, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 648805, 717, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 649622, 717, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 650439, 717, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 651256, 717, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 652073, 717, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 652890, 717, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 653707, 717, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 654524, 717, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 655341, 717, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 656158, 717, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 656975, 717, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 657792, 717, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 658609, 717, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 659426, 717, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 660243, 717, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 661060, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP20.m new file mode 100644 index 0000000..49fc596 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP20.m @@ -0,0 +1,531 @@ +classdef SingleGFP20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFP20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 588347, 717, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 589164, 717, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 589981, 717, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 590798, 717, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 591615, 717, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 592432, 717, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 593249, 717, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 594066, 717, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 594883, 717, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 595700, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP5.m new file mode 100644 index 0000000..9605790 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP5.m @@ -0,0 +1,171 @@ +classdef SingleGFP5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFP5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP50.m new file mode 100644 index 0000000..3af0dc4 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFP50.m @@ -0,0 +1,1251 @@ +classdef SingleGFP50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFP50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 588347, 717, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 589164, 717, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 589981, 717, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 590798, 717, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 591615, 717, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 592432, 717, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 593249, 717, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 594066, 717, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 594883, 717, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 595700, 717, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 596517, 717, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 597334, 717, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 598151, 717, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 598968, 717, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 599785, 717, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 600602, 717, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 601419, 717, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 602236, 717, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 603053, 717, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 603870, 717, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 604687, 717, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 605504, 717, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 606321, 717, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 607138, 717, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 607955, 717, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 608772, 717, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 609589, 717, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 610406, 717, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 611223, 717, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 612040, 717, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 612857, 717, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 613674, 717, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 614491, 717, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 615308, 717, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 616125, 717, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 616942, 717, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 617759, 717, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 618576, 717, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 619393, 717, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 620210, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized1.m new file mode 100644 index 0000000..76ea2a3 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized1.m @@ -0,0 +1,75 @@ +classdef SingleGFPOptimized1 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFPOptimized1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCAAAAGGTGAAGAATTATTTACTGGTGTTGTTCCTATTTTAGTTGAATTAGATGGTGATGTTAATGGTCATAAATTTTCAGTTTCAGGTGAAGGTGAAGGTGATGCTACTTATGGTAAATTAACTTTAAAATTTATTTGTACTACTGGTAAATTACCTGTTCCTTGGCCTACTTTAGTTACTACTTTTGGTTATGGTGTTCAATGTTTTGCTAGATATCCTGATCATATGAAACAACATGATTTTTTTAAATCAGCTATGCCTGAAGGTTATGTTCAAGAAAGAACTATTTTTTTTAAAGATGATGGTAATTATAAAACTAGAGCTGAAGTTAAATTTGAAGGTGATACTTTAGTTAATAGAATTGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAATATTTTAGGTCATAAATTAGAATATAATTATAATTCACATAATGTTTATATTATGGCTGATAAACAAAAAAATGGTATTAAAGTTAATTTTAAAATTAGACATAATATTGAAGATGGTTCAGTTCAATTAGCTGATCATTATCAACAAAATACTCCTATTGGTGATGGTCCTGTTTTATTACCTGATAATCATTATTTATCAACTCAATCAGCTTTATCAAAAGATCCTAATGAAAAAAGAGATCATATGGTTTTATTAGAATTTGTTACTGCTGCTGGTATTACTCATGGTATGGATGAATTATATAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized10.m new file mode 100644 index 0000000..1ee7d33 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized10.m @@ -0,0 +1,291 @@ +classdef SingleGFPOptimized10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFPOptimized10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCAAAAGGTGAAGAATTATTTACTGGTGTTGTTCCTATTTTAGTTGAATTAGATGGTGATGTTAATGGTCATAAATTTTCAGTTTCAGGTGAAGGTGAAGGTGATGCTACTTATGGTAAATTAACTTTAAAATTTATTTGTACTACTGGTAAATTACCTGTTCCTTGGCCTACTTTAGTTACTACTTTTGGTTATGGTGTTCAATGTTTTGCTAGATATCCTGATCATATGAAACAACATGATTTTTTTAAATCAGCTATGCCTGAAGGTTATGTTCAAGAAAGAACTATTTTTTTTAAAGATGATGGTAATTATAAAACTAGAGCTGAAGTTAAATTTGAAGGTGATACTTTAGTTAATAGAATTGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAATATTTTAGGTCATAAATTAGAATATAATTATAATTCACATAATGTTTATATTATGGCTGATAAACAAAAAAATGGTATTAAAGTTAATTTTAAAATTAGACATAATATTGAAGATGGTTCAGTTCAATTAGCTGATCATTATCAACAAAATACTCCTATTGGTGATGGTCCTGTTTTATTACCTGATAATCATTATTTATCAACTCAATCAGCTTTATCAAAAGATCCTAATGAAAAAAGAGATCATATGGTTTTATTAGAATTTGTTACTGCTGCTGGTATTACTCATGGTATGGATGAATTATATAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized100.m new file mode 100644 index 0000000..9789ad6 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized100.m @@ -0,0 +1,2451 @@ +classdef SingleGFPOptimized100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFPOptimized100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 588347, 717, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 589164, 717, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 589981, 717, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 590798, 717, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 591615, 717, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 592432, 717, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 593249, 717, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 594066, 717, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 594883, 717, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 595700, 717, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 596517, 717, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 597334, 717, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 598151, 717, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 598968, 717, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 599785, 717, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 600602, 717, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 601419, 717, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 602236, 717, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 603053, 717, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 603870, 717, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 604687, 717, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 605504, 717, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 606321, 717, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 607138, 717, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 607955, 717, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 608772, 717, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 609589, 717, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 610406, 717, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 611223, 717, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 612040, 717, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 612857, 717, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 613674, 717, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 614491, 717, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 615308, 717, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 616125, 717, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 616942, 717, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 617759, 717, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 618576, 717, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 619393, 717, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 620210, 717, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 621027, 717, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 621844, 717, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 622661, 717, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 623478, 717, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 624295, 717, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 625112, 717, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 625929, 717, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 626746, 717, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 627563, 717, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 628380, 717, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 629197, 717, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 630014, 717, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 630831, 717, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 631648, 717, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 632465, 717, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 633282, 717, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 634099, 717, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 634916, 717, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 635733, 717, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 636550, 717, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 637367, 717, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 638184, 717, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 639001, 717, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 639818, 717, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 640635, 717, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 641452, 717, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 642269, 717, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 643086, 717, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 643903, 717, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 644720, 717, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 645537, 717, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 646354, 717, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 647171, 717, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 647988, 717, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 648805, 717, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 649622, 717, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 650439, 717, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 651256, 717, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 652073, 717, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 652890, 717, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 653707, 717, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 654524, 717, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 655341, 717, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 656158, 717, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 656975, 717, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 657792, 717, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 658609, 717, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 659426, 717, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 660243, 717, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 661060, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCAAAAGGTGAAGAATTATTTACTGGTGTTGTTCCTATTTTAGTTGAATTAGATGGTGATGTTAATGGTCATAAATTTTCAGTTTCAGGTGAAGGTGAAGGTGATGCTACTTATGGTAAATTAACTTTAAAATTTATTTGTACTACTGGTAAATTACCTGTTCCTTGGCCTACTTTAGTTACTACTTTTGGTTATGGTGTTCAATGTTTTGCTAGATATCCTGATCATATGAAACAACATGATTTTTTTAAATCAGCTATGCCTGAAGGTTATGTTCAAGAAAGAACTATTTTTTTTAAAGATGATGGTAATTATAAAACTAGAGCTGAAGTTAAATTTGAAGGTGATACTTTAGTTAATAGAATTGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAATATTTTAGGTCATAAATTAGAATATAATTATAATTCACATAATGTTTATATTATGGCTGATAAACAAAAAAATGGTATTAAAGTTAATTTTAAAATTAGACATAATATTGAAGATGGTTCAGTTCAATTAGCTGATCATTATCAACAAAATACTCCTATTGGTGATGGTCCTGTTTTATTACCTGATAATCATTATTTATCAACTCAATCAGCTTTATCAAAAGATCCTAATGAAAAAAGAGATCATATGGTTTTATTAGAATTTGTTACTGCTGCTGGTATTACTCATGGTATGGATGAATTATATAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized20.m new file mode 100644 index 0000000..2bdfd27 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized20.m @@ -0,0 +1,531 @@ +classdef SingleGFPOptimized20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFPOptimized20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 588347, 717, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 589164, 717, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 589981, 717, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 590798, 717, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 591615, 717, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 592432, 717, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 593249, 717, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 594066, 717, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 594883, 717, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 595700, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCAAAAGGTGAAGAATTATTTACTGGTGTTGTTCCTATTTTAGTTGAATTAGATGGTGATGTTAATGGTCATAAATTTTCAGTTTCAGGTGAAGGTGAAGGTGATGCTACTTATGGTAAATTAACTTTAAAATTTATTTGTACTACTGGTAAATTACCTGTTCCTTGGCCTACTTTAGTTACTACTTTTGGTTATGGTGTTCAATGTTTTGCTAGATATCCTGATCATATGAAACAACATGATTTTTTTAAATCAGCTATGCCTGAAGGTTATGTTCAAGAAAGAACTATTTTTTTTAAAGATGATGGTAATTATAAAACTAGAGCTGAAGTTAAATTTGAAGGTGATACTTTAGTTAATAGAATTGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAATATTTTAGGTCATAAATTAGAATATAATTATAATTCACATAATGTTTATATTATGGCTGATAAACAAAAAAATGGTATTAAAGTTAATTTTAAAATTAGACATAATATTGAAGATGGTTCAGTTCAATTAGCTGATCATTATCAACAAAATACTCCTATTGGTGATGGTCCTGTTTTATTACCTGATAATCATTATTTATCAACTCAATCAGCTTTATCAAAAGATCCTAATGAAAAAAGAGATCATATGGTTTTATTAGAATTTGTTACTGCTGCTGGTATTACTCATGGTATGGATGAATTATATAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized5.m new file mode 100644 index 0000000..26432f8 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized5.m @@ -0,0 +1,171 @@ +classdef SingleGFPOptimized5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFPOptimized5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCAAAAGGTGAAGAATTATTTACTGGTGTTGTTCCTATTTTAGTTGAATTAGATGGTGATGTTAATGGTCATAAATTTTCAGTTTCAGGTGAAGGTGAAGGTGATGCTACTTATGGTAAATTAACTTTAAAATTTATTTGTACTACTGGTAAATTACCTGTTCCTTGGCCTACTTTAGTTACTACTTTTGGTTATGGTGTTCAATGTTTTGCTAGATATCCTGATCATATGAAACAACATGATTTTTTTAAATCAGCTATGCCTGAAGGTTATGTTCAAGAAAGAACTATTTTTTTTAAAGATGATGGTAATTATAAAACTAGAGCTGAAGTTAAATTTGAAGGTGATACTTTAGTTAATAGAATTGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAATATTTTAGGTCATAAATTAGAATATAATTATAATTCACATAATGTTTATATTATGGCTGATAAACAAAAAAATGGTATTAAAGTTAATTTTAAAATTAGACATAATATTGAAGATGGTTCAGTTCAATTAGCTGATCATTATCAACAAAATACTCCTATTGGTGATGGTCCTGTTTTATTACCTGATAATCATTATTTATCAACTCAATCAGCTTTATCAAAAGATCCTAATGAAAAAAGAGATCATATGGTTTTATTAGAATTTGTTACTGCTGCTGGTATTACTCATGGTATGGATGAATTATATAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized50.m new file mode 100644 index 0000000..4de0f4c --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingleGFPOptimized50.m @@ -0,0 +1,1251 @@ +classdef SingleGFPOptimized50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGFPOptimized50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 717, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580994, 717, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581811, 717, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582628, 717, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583445, 717, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 584262, 717, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 585079, 717, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585896, 717, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 586713, 717, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 587530, 717, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 588347, 717, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 589164, 717, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 589981, 717, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 590798, 717, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 591615, 717, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 592432, 717, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 593249, 717, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 594066, 717, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 594883, 717, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 595700, 717, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 596517, 717, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 597334, 717, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 598151, 717, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 598968, 717, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 599785, 717, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 600602, 717, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 601419, 717, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 602236, 717, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 603053, 717, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 603870, 717, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 604687, 717, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 605504, 717, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 606321, 717, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 607138, 717, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 607955, 717, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 608772, 717, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 609589, 717, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 610406, 717, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 611223, 717, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 612040, 717, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 612857, 717, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 613674, 717, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 614491, 717, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 615308, 717, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 616125, 717, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 616942, 717, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 617759, 717, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 618576, 717, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 619393, 717, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 620210, 717, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gfp = 'ATGTCAAAAGGTGAAGAATTATTTACTGGTGTTGTTCCTATTTTAGTTGAATTAGATGGTGATGTTAATGGTCATAAATTTTCAGTTTCAGGTGAAGGTGAAGGTGATGCTACTTATGGTAAATTAACTTTAAAATTTATTTGTACTACTGGTAAATTACCTGTTCCTTGGCCTACTTTAGTTACTACTTTTGGTTATGGTGTTCAATGTTTTGCTAGATATCCTGATCATATGAAACAACATGATTTTTTTAAATCAGCTATGCCTGAAGGTTATGTTCAAGAAAGAACTATTTTTTTTAAAGATGATGGTAATTATAAAACTAGAGCTGAAGTTAAATTTGAAGGTGATACTTTAGTTAATAGAATTGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAATATTTTAGGTCATAAATTAGAATATAATTATAATTCACATAATGTTTATATTATGGCTGATAAACAAAAAAATGGTATTAAAGTTAATTTTAAAATTAGACATAATATTGAAGATGGTTCAGTTCAATTAGCTGATCATTATCAACAAAATACTCCTATTGGTGATGGTCCTGTTTTATTACCTGATAATCATTATTTATCAACTCAATCAGCTTTATCAAAAGATCCTAATGAAAAAAGAGATCATATGGTTTTATTAGAATTTGTTACTGCTGCTGGTATTACTCATGGTATGGATGAATTATATAAATAA'; + genome.sequence = [genome.sequence repmat([promoter gfp], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC1.m new file mode 100644 index 0000000..dfbe791 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC1.m @@ -0,0 +1,75 @@ +classdef SinglearaC1 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaC1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAATGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTTTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGGTTCTTTCGCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGGGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTCCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC10.m new file mode 100644 index 0000000..5eb78b8 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC10.m @@ -0,0 +1,291 @@ +classdef SinglearaC10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaC10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAATGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTTTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGGTTCTTTCGCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGGGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTCCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC100.m new file mode 100644 index 0000000..d20c39c --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC100.m @@ -0,0 +1,2451 @@ +classdef SinglearaC100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaC100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 589967, 879, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 590946, 879, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 591925, 879, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 592904, 879, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 593883, 879, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 594862, 879, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 595841, 879, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 596820, 879, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 597799, 879, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 598778, 879, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 599757, 879, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 600736, 879, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 601715, 879, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 602694, 879, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 603673, 879, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 604652, 879, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 605631, 879, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 606610, 879, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 607589, 879, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 608568, 879, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 609547, 879, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 610526, 879, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 611505, 879, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 612484, 879, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 613463, 879, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 614442, 879, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 615421, 879, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 616400, 879, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 617379, 879, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 618358, 879, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 619337, 879, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 620316, 879, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 621295, 879, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 622274, 879, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 623253, 879, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 624232, 879, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 625211, 879, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 626190, 879, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 627169, 879, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 628148, 879, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 629127, 879, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 630106, 879, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 631085, 879, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 632064, 879, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 633043, 879, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 634022, 879, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 635001, 879, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 635980, 879, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 636959, 879, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 637938, 879, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 638917, 879, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 639896, 879, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 640875, 879, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 641854, 879, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 642833, 879, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 643812, 879, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 644791, 879, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 645770, 879, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 646749, 879, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 647728, 879, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 648707, 879, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 649686, 879, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 650665, 879, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 651644, 879, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 652623, 879, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 653602, 879, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 654581, 879, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 655560, 879, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 656539, 879, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 657518, 879, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 658497, 879, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 659476, 879, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 660455, 879, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 661434, 879, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 662413, 879, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 663392, 879, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 664371, 879, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 665350, 879, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 666329, 879, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 667308, 879, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 668287, 879, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 669266, 879, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 670245, 879, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 671224, 879, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 672203, 879, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 673182, 879, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 674161, 879, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 675140, 879, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 676119, 879, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 677098, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAATGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTTTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGGTTCTTTCGCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGGGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTCCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC20.m new file mode 100644 index 0000000..30f42cb --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC20.m @@ -0,0 +1,531 @@ +classdef SinglearaC20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaC20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 589967, 879, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 590946, 879, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 591925, 879, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 592904, 879, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 593883, 879, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 594862, 879, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 595841, 879, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 596820, 879, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 597799, 879, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 598778, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAATGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTTTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGGTTCTTTCGCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGGGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTCCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC5.m new file mode 100644 index 0000000..cdd54c0 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC5.m @@ -0,0 +1,171 @@ +classdef SinglearaC5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaC5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAATGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTTTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGGTTCTTTCGCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGGGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTCCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC50.m new file mode 100644 index 0000000..28d605f --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaC50.m @@ -0,0 +1,1251 @@ +classdef SinglearaC50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaC50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 589967, 879, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 590946, 879, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 591925, 879, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 592904, 879, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 593883, 879, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 594862, 879, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 595841, 879, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 596820, 879, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 597799, 879, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 598778, 879, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 599757, 879, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 600736, 879, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 601715, 879, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 602694, 879, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 603673, 879, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 604652, 879, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 605631, 879, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 606610, 879, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 607589, 879, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 608568, 879, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 609547, 879, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 610526, 879, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 611505, 879, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 612484, 879, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 613463, 879, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 614442, 879, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 615421, 879, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 616400, 879, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 617379, 879, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 618358, 879, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 619337, 879, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 620316, 879, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 621295, 879, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 622274, 879, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 623253, 879, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 624232, 879, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 625211, 879, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 626190, 879, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 627169, 879, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 628148, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAATGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTTTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGGTTCTTTCGCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGGGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTCCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized1.m new file mode 100644 index 0000000..5510995 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized1.m @@ -0,0 +1,75 @@ +classdef SinglearaCOptimized1 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaCOptimized1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCTCAAAATGATCCTTTATTACCTGGTTATTCATTTAATGCTCATTTAGTTGCTGGTTTAACTCCTATTGAAGCTAATGGTTATTTAGATTTTTTTATTGATAGACCTTTAGGTATGAAAGGTTATATTTTAAATTTAACTATTAGAGGTCAAGGTGTTGTTAAAAATCAAGGTAGAGAATTTGTTTGTAGACCTGGTGATATTTTATTATTTCCTCCTGGTGAAATTCATCATTATGGTAGACATCCTGAAGCTAGAGAATGGTATCATCAATGGGTTTATTTTAGACCTAGAGCTTATTGGCATGAATGGTTAAATTGGCCTTCAATTTTTGCTAATACTGGTTTTTTTAGACCTGATGAAGCTCATCAACCTCATTTTTCAGATTTATTTGGTCAAATTATTAATGCTGGTCAAGGTGAAGGTAGATATTCAGAATTATTAGCTATTAATTTATTAGAACAATTATTATTAAGAAGAATGGAAGCTATTAATGAATCATTACATCCTCCTATGGATAATAGAGTTAGAGAAGCTTGTCAATATATTTCAGATCATTTAGCTGATTCAAATTTTGATATTGCTTCAGTTGCTCAACATGTTTGTTTATCACCTTCAAGATTATCACATTTATTTAGACAACAATTAGGTATTTCAGTTTTATCATGGAGAGAAGATCAAAGAATTTCACAAGCTAAATTATTATTATCAACTACTAGAATGCCTATTGCTACTGTTGGTAGAAATGTTGGTTTTGATGATCAATTATATTTTTCAAGAGTTTTTAAAAAATGTACTGGTGCTTCACCTTCAGAATTTAGAGCTGGTTGTGAAGAAAAAGTTAATGATGTTGCTGTTAAATTATCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized10.m new file mode 100644 index 0000000..cef5e40 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized10.m @@ -0,0 +1,291 @@ +classdef SinglearaCOptimized10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaCOptimized10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCTCAAAATGATCCTTTATTACCTGGTTATTCATTTAATGCTCATTTAGTTGCTGGTTTAACTCCTATTGAAGCTAATGGTTATTTAGATTTTTTTATTGATAGACCTTTAGGTATGAAAGGTTATATTTTAAATTTAACTATTAGAGGTCAAGGTGTTGTTAAAAATCAAGGTAGAGAATTTGTTTGTAGACCTGGTGATATTTTATTATTTCCTCCTGGTGAAATTCATCATTATGGTAGACATCCTGAAGCTAGAGAATGGTATCATCAATGGGTTTATTTTAGACCTAGAGCTTATTGGCATGAATGGTTAAATTGGCCTTCAATTTTTGCTAATACTGGTTTTTTTAGACCTGATGAAGCTCATCAACCTCATTTTTCAGATTTATTTGGTCAAATTATTAATGCTGGTCAAGGTGAAGGTAGATATTCAGAATTATTAGCTATTAATTTATTAGAACAATTATTATTAAGAAGAATGGAAGCTATTAATGAATCATTACATCCTCCTATGGATAATAGAGTTAGAGAAGCTTGTCAATATATTTCAGATCATTTAGCTGATTCAAATTTTGATATTGCTTCAGTTGCTCAACATGTTTGTTTATCACCTTCAAGATTATCACATTTATTTAGACAACAATTAGGTATTTCAGTTTTATCATGGAGAGAAGATCAAAGAATTTCACAAGCTAAATTATTATTATCAACTACTAGAATGCCTATTGCTACTGTTGGTAGAAATGTTGGTTTTGATGATCAATTATATTTTTCAAGAGTTTTTAAAAAATGTACTGGTGCTTCACCTTCAGAATTTAGAGCTGGTTGTGAAGAAAAAGTTAATGATGTTGCTGTTAAATTATCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized100.m new file mode 100644 index 0000000..6f44655 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized100.m @@ -0,0 +1,2451 @@ +classdef SinglearaCOptimized100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaCOptimized100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 589967, 879, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 590946, 879, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 591925, 879, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 592904, 879, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 593883, 879, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 594862, 879, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 595841, 879, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 596820, 879, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 597799, 879, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 598778, 879, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 599757, 879, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 600736, 879, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 601715, 879, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 602694, 879, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 603673, 879, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 604652, 879, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 605631, 879, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 606610, 879, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 607589, 879, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 608568, 879, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 609547, 879, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 610526, 879, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 611505, 879, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 612484, 879, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 613463, 879, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 614442, 879, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 615421, 879, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 616400, 879, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 617379, 879, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 618358, 879, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 619337, 879, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 620316, 879, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 621295, 879, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 622274, 879, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 623253, 879, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 624232, 879, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 625211, 879, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 626190, 879, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 627169, 879, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 628148, 879, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 629127, 879, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 630106, 879, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 631085, 879, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 632064, 879, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 633043, 879, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 634022, 879, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 635001, 879, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 635980, 879, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 636959, 879, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 637938, 879, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 638917, 879, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 639896, 879, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 640875, 879, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 641854, 879, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 642833, 879, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 643812, 879, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 644791, 879, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 645770, 879, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 646749, 879, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 647728, 879, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 648707, 879, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 649686, 879, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 650665, 879, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 651644, 879, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 652623, 879, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 653602, 879, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 654581, 879, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 655560, 879, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 656539, 879, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 657518, 879, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 658497, 879, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 659476, 879, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 660455, 879, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 661434, 879, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 662413, 879, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 663392, 879, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 664371, 879, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 665350, 879, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 666329, 879, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 667308, 879, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 668287, 879, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 669266, 879, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 670245, 879, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 671224, 879, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 672203, 879, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 673182, 879, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 674161, 879, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 675140, 879, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 676119, 879, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 677098, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCTCAAAATGATCCTTTATTACCTGGTTATTCATTTAATGCTCATTTAGTTGCTGGTTTAACTCCTATTGAAGCTAATGGTTATTTAGATTTTTTTATTGATAGACCTTTAGGTATGAAAGGTTATATTTTAAATTTAACTATTAGAGGTCAAGGTGTTGTTAAAAATCAAGGTAGAGAATTTGTTTGTAGACCTGGTGATATTTTATTATTTCCTCCTGGTGAAATTCATCATTATGGTAGACATCCTGAAGCTAGAGAATGGTATCATCAATGGGTTTATTTTAGACCTAGAGCTTATTGGCATGAATGGTTAAATTGGCCTTCAATTTTTGCTAATACTGGTTTTTTTAGACCTGATGAAGCTCATCAACCTCATTTTTCAGATTTATTTGGTCAAATTATTAATGCTGGTCAAGGTGAAGGTAGATATTCAGAATTATTAGCTATTAATTTATTAGAACAATTATTATTAAGAAGAATGGAAGCTATTAATGAATCATTACATCCTCCTATGGATAATAGAGTTAGAGAAGCTTGTCAATATATTTCAGATCATTTAGCTGATTCAAATTTTGATATTGCTTCAGTTGCTCAACATGTTTGTTTATCACCTTCAAGATTATCACATTTATTTAGACAACAATTAGGTATTTCAGTTTTATCATGGAGAGAAGATCAAAGAATTTCACAAGCTAAATTATTATTATCAACTACTAGAATGCCTATTGCTACTGTTGGTAGAAATGTTGGTTTTGATGATCAATTATATTTTTCAAGAGTTTTTAAAAAATGTACTGGTGCTTCACCTTCAGAATTTAGAGCTGGTTGTGAAGAAAAAGTTAATGATGTTGCTGTTAAATTATCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized20.m new file mode 100644 index 0000000..7f0e02d --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized20.m @@ -0,0 +1,531 @@ +classdef SinglearaCOptimized20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaCOptimized20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 589967, 879, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 590946, 879, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 591925, 879, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 592904, 879, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 593883, 879, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 594862, 879, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 595841, 879, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 596820, 879, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 597799, 879, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 598778, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCTCAAAATGATCCTTTATTACCTGGTTATTCATTTAATGCTCATTTAGTTGCTGGTTTAACTCCTATTGAAGCTAATGGTTATTTAGATTTTTTTATTGATAGACCTTTAGGTATGAAAGGTTATATTTTAAATTTAACTATTAGAGGTCAAGGTGTTGTTAAAAATCAAGGTAGAGAATTTGTTTGTAGACCTGGTGATATTTTATTATTTCCTCCTGGTGAAATTCATCATTATGGTAGACATCCTGAAGCTAGAGAATGGTATCATCAATGGGTTTATTTTAGACCTAGAGCTTATTGGCATGAATGGTTAAATTGGCCTTCAATTTTTGCTAATACTGGTTTTTTTAGACCTGATGAAGCTCATCAACCTCATTTTTCAGATTTATTTGGTCAAATTATTAATGCTGGTCAAGGTGAAGGTAGATATTCAGAATTATTAGCTATTAATTTATTAGAACAATTATTATTAAGAAGAATGGAAGCTATTAATGAATCATTACATCCTCCTATGGATAATAGAGTTAGAGAAGCTTGTCAATATATTTCAGATCATTTAGCTGATTCAAATTTTGATATTGCTTCAGTTGCTCAACATGTTTGTTTATCACCTTCAAGATTATCACATTTATTTAGACAACAATTAGGTATTTCAGTTTTATCATGGAGAGAAGATCAAAGAATTTCACAAGCTAAATTATTATTATCAACTACTAGAATGCCTATTGCTACTGTTGGTAGAAATGTTGGTTTTGATGATCAATTATATTTTTCAAGAGTTTTTAAAAAATGTACTGGTGCTTCACCTTCAGAATTTAGAGCTGGTTGTGAAGAAAAAGTTAATGATGTTGCTGTTAAATTATCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized5.m new file mode 100644 index 0000000..bae1452 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized5.m @@ -0,0 +1,171 @@ +classdef SinglearaCOptimized5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaCOptimized5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCTCAAAATGATCCTTTATTACCTGGTTATTCATTTAATGCTCATTTAGTTGCTGGTTTAACTCCTATTGAAGCTAATGGTTATTTAGATTTTTTTATTGATAGACCTTTAGGTATGAAAGGTTATATTTTAAATTTAACTATTAGAGGTCAAGGTGTTGTTAAAAATCAAGGTAGAGAATTTGTTTGTAGACCTGGTGATATTTTATTATTTCCTCCTGGTGAAATTCATCATTATGGTAGACATCCTGAAGCTAGAGAATGGTATCATCAATGGGTTTATTTTAGACCTAGAGCTTATTGGCATGAATGGTTAAATTGGCCTTCAATTTTTGCTAATACTGGTTTTTTTAGACCTGATGAAGCTCATCAACCTCATTTTTCAGATTTATTTGGTCAAATTATTAATGCTGGTCAAGGTGAAGGTAGATATTCAGAATTATTAGCTATTAATTTATTAGAACAATTATTATTAAGAAGAATGGAAGCTATTAATGAATCATTACATCCTCCTATGGATAATAGAGTTAGAGAAGCTTGTCAATATATTTCAGATCATTTAGCTGATTCAAATTTTGATATTGCTTCAGTTGCTCAACATGTTTGTTTATCACCTTCAAGATTATCACATTTATTTAGACAACAATTAGGTATTTCAGTTTTATCATGGAGAGAAGATCAAAGAATTTCACAAGCTAAATTATTATTATCAACTACTAGAATGCCTATTGCTACTGTTGGTAGAAATGTTGGTTTTGATGATCAATTATATTTTTCAAGAGTTTTTAAAAAATGTACTGGTGCTTCACCTTCAGAATTTAGAGCTGGTTGTGAAGAAAAAGTTAATGATGTTGCTGTTAAATTATCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized50.m new file mode 100644 index 0000000..0dde0a6 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglearaCOptimized50.m @@ -0,0 +1,1251 @@ +classdef SinglearaCOptimized50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SinglearaCOptimized50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 879, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581156, 879, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582135, 879, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583114, 879, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584093, 879, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 585072, 879, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 586051, 879, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 587030, 879, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 588009, 879, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 588988, 879, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 589967, 879, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 590946, 879, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 591925, 879, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 592904, 879, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 593883, 879, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 594862, 879, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 595841, 879, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 596820, 879, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 597799, 879, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 598778, 879, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 599757, 879, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 600736, 879, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 601715, 879, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 602694, 879, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 603673, 879, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 604652, 879, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 605631, 879, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 606610, 879, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 607589, 879, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 608568, 879, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 609547, 879, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 610526, 879, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 611505, 879, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 612484, 879, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 613463, 879, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 614442, 879, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 615421, 879, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 616400, 879, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 617379, 879, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 618358, 879, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 619337, 879, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 620316, 879, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 621295, 879, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 622274, 879, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 623253, 879, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 624232, 879, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 625211, 879, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 626190, 879, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 627169, 879, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 628148, 879, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGGCTGAAGCTCAAAATGATCCTTTATTACCTGGTTATTCATTTAATGCTCATTTAGTTGCTGGTTTAACTCCTATTGAAGCTAATGGTTATTTAGATTTTTTTATTGATAGACCTTTAGGTATGAAAGGTTATATTTTAAATTTAACTATTAGAGGTCAAGGTGTTGTTAAAAATCAAGGTAGAGAATTTGTTTGTAGACCTGGTGATATTTTATTATTTCCTCCTGGTGAAATTCATCATTATGGTAGACATCCTGAAGCTAGAGAATGGTATCATCAATGGGTTTATTTTAGACCTAGAGCTTATTGGCATGAATGGTTAAATTGGCCTTCAATTTTTGCTAATACTGGTTTTTTTAGACCTGATGAAGCTCATCAACCTCATTTTTCAGATTTATTTGGTCAAATTATTAATGCTGGTCAAGGTGAAGGTAGATATTCAGAATTATTAGCTATTAATTTATTAGAACAATTATTATTAAGAAGAATGGAAGCTATTAATGAATCATTACATCCTCCTATGGATAATAGAGTTAGAGAAGCTTGTCAATATATTTCAGATCATTTAGCTGATTCAAATTTTGATATTGCTTCAGTTGCTCAACATGTTTGTTTATCACCTTCAAGATTATCACATTTATTTAGACAACAATTAGGTATTTCAGTTTTATCATGGAGAGAAGATCAAAGAATTTCACAAGCTAAATTATTATTATCAACTACTAGAATGCCTATTGCTACTGTTGGTAGAAATGTTGGTTTTGATGATCAATTATATTTTTCAAGAGTTTTTAAAAAATGTACTGGTGCTTCACCTTCAGAATTTAGAGCTGGTTGTGAAGAAAAAGTTAATGATGTTGCTGTTAAATTATCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI1.m new file mode 100644 index 0000000..2d2e5ec --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI1.m @@ -0,0 +1,120 @@ +% Instantiate simulation from modified knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Author: Bonny Jain, bonny.jain@mit.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SingleGene < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + + %% create new genes, transcription units, etc. + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); %normal, cold shock, heat shock + geneA = Gene(kb, NaN, {'GeneA'}, {'Gene A'}, {'genA'}, {''}, {'mRNA'}, 0, {''}, ... + 580177, 1083, true, {''}, meanHL, expression); + + tuA = TranscriptionUnit(kb, NaN, {'TuA'}, {'Transcription unit A'},... + -35, 6, ... + -10, 6, ... + -1); + + monA = ProteinMonomer(kb, NaN, {'MonomerA'}, {'Protein monomer A'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + cpxAA = ProteinComplex(kb, NaN, {'ComplexAA'}, {'Macromolecular complex AA'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence promoter lacI]; + genome.sequenceLength = length(genome.sequence); + + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + + %% create new relationships among new genes, transcription units, etc. + geneA.genome = genome; + geneA.transcriptionUnits = tuA; + geneA.proteinMonomers = monA; + geneA.compartment = cytosol; + + tuA.genome = genome; + tuA.genes = geneA; + tuA.geneCompartments = cytosol; + tuA.compartment = cytosol; + + monA.gene = geneA; + monA.geneCompartments = cytosol; + monA.compartment = cytosol; + + cpxAA.proteinMonomers = monA; + cpxAA.proteinMonomerCompartments = cytosol; + cpxAA.proteinMonomerCoefficients = 4; + cpxAA.compartment = cytosol; + cpxAA.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA]; + + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA]; + + %% class super class method + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + + function modifyNetworkParameters(~, sim) + %% get handles + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + + %% get constants + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + + %% get parameter values + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + + %% calculate modified parameter values + %set binding probability of new TUs + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + + %renormalize + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + + %update expression + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + + %% update parameter values + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI10.m new file mode 100644 index 0000000..aebb489 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI10.m @@ -0,0 +1,482 @@ +% Instantiate simulation from modified knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Author: Bonny Jain, bonny.jain@mit.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SingleGene10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + + %% create new genes, transcription units, etc. + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); %normal, cold shock, heat shock + + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, ... + 580177, 1083, true, {''}, meanHL, expression); + + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, ... + 581360, 1083, true, {''}, meanHL, expression); + + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, ... + 582543, 1083, true, {''}, meanHL, expression); + + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, ... + 583726, 1083, true, {''}, meanHL, expression); + + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, ... + 584909, 1083, true, {''}, meanHL, expression); + + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, ... + 585092, 1083, true, {''}, meanHL, expression); + + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, ... + 587275, 1083, true, {''}, meanHL, expression); + + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, ... + 588458, 1083, true, {''}, meanHL, expression); + + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, ... + 589641, 1083, true, {''}, meanHL, expression); + + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, ... + 590824, 1083, true, {''}, meanHL, expression); + + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'},... + -35, 6, ... + -10, 6, ... + -1); + + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + + %% create new relationships among new genes, transcription units, etc. + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + + %% class super class method + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + + function modifyNetworkParameters(~, sim) + %% get handles + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + + %% get constants + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + + %% get parameter values + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + + %% calculate modified parameter values + %set binding probability of new TUs + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + + %renormalize + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + + %update expression + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + + %% update parameter values + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI100.m new file mode 100644 index 0000000..9063259 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI100.m @@ -0,0 +1,2451 @@ +classdef SingleGene100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 1083, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581360, 1083, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582543, 1083, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583726, 1083, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584909, 1083, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 586092, 1083, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 587275, 1083, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 588458, 1083, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 589641, 1083, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 590824, 1083, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 592007, 1083, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 593190, 1083, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 594373, 1083, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 595556, 1083, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 596739, 1083, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 597922, 1083, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 599105, 1083, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 600288, 1083, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 601471, 1083, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 602654, 1083, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 603837, 1083, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 605020, 1083, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 606203, 1083, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 607386, 1083, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 608569, 1083, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 609752, 1083, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 610935, 1083, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 612118, 1083, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 613301, 1083, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 614484, 1083, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 615667, 1083, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 616850, 1083, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 618033, 1083, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 619216, 1083, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 620399, 1083, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 621582, 1083, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 622765, 1083, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 623948, 1083, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 625131, 1083, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 626314, 1083, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 627497, 1083, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 628680, 1083, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 629863, 1083, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 631046, 1083, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 632229, 1083, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 633412, 1083, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 634595, 1083, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 635778, 1083, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 636961, 1083, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 638144, 1083, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 639327, 1083, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 640510, 1083, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 641693, 1083, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 642876, 1083, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 644059, 1083, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 645242, 1083, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 646425, 1083, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 647608, 1083, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 648791, 1083, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 649974, 1083, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 651157, 1083, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 652340, 1083, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 653523, 1083, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 654706, 1083, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 655889, 1083, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 657072, 1083, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 658255, 1083, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 659438, 1083, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 660621, 1083, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 661804, 1083, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 662987, 1083, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 664170, 1083, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 665353, 1083, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 666536, 1083, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 667719, 1083, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 668902, 1083, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 670085, 1083, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 671268, 1083, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 672451, 1083, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 673634, 1083, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 674817, 1083, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 676000, 1083, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 677183, 1083, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 678366, 1083, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 679549, 1083, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 680732, 1083, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 681915, 1083, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 683098, 1083, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 684281, 1083, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 685464, 1083, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 686647, 1083, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 687830, 1083, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 689013, 1083, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 690196, 1083, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 691379, 1083, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 692562, 1083, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 693745, 1083, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 694928, 1083, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 696111, 1083, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 697294, 1083, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI20.m new file mode 100644 index 0000000..ebbac14 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI20.m @@ -0,0 +1,531 @@ +classdef SingleGene20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 1083, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581360, 1083, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582543, 1083, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583726, 1083, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584909, 1083, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 586092, 1083, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 587275, 1083, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 588458, 1083, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 589641, 1083, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 590824, 1083, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 592007, 1083, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 593190, 1083, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 594373, 1083, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 595556, 1083, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 596739, 1083, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 597922, 1083, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 599105, 1083, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 600288, 1083, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 601471, 1083, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 602654, 1083, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA2.gene = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + monA3.gene = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + monA4.gene = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + monA5.gene = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA6.gene = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + monA7.gene = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + monA8.gene = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + monA9.gene = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + monA10.gene = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA11.gene = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + monA12.gene = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + monA13.gene = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + monA14.gene = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + monA15.gene = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + monA16.gene = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + monA17.gene = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + monA18.gene = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + monA19.gene = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + monA20.gene = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({TuA1, TuA2, TuA3, TuA4, TuA5, TuA6, TuA7, TuA8, TuA9, TuA10, TuA11, TuA12, TuA13, TuA14, TuA15, TuA16, TuA17, TuA18, TuA19, TuA20}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI5.m new file mode 100644 index 0000000..7e24581 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI5.m @@ -0,0 +1,280 @@ +% Instantiate simulation from modified knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Author: Bonny Jain, bonny.jain@mit.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SingleGene5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + + %% create new genes, transcription units, etc. + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); %normal, cold shock, heat shock + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, ... + 580177, 1083, true, {''}, meanHL, expression); + + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, ... + 581360, 1083, true, {''}, meanHL, expression); + + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, ... + 582543, 1083, true, {''}, meanHL, expression); + + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, ... + 583726, 1083, true, {''}, meanHL, expression); + + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, ... + 584909, 1083, true, {''}, meanHL, expression); + + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'},... + -35, 6, ... + -10, 6, ... + -1); + + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + + %% create new relationships among new genes, transcription units, etc. + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + + %% class super class method + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + + function modifyNetworkParameters(~, sim) + %% get handles + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + + %% get constants + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + + %% get parameter values + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + + %% calculate modified parameter values + %set binding probability of new TUs + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + + %renormalize + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + + %update expression + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + + %% update parameter values + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI50.m new file mode 100644 index 0000000..bc588e9 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacI50.m @@ -0,0 +1,1251 @@ +classdef SingleGene50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 1083, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581360, 1083, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582543, 1083, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583726, 1083, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584909, 1083, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 586092, 1083, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 587275, 1083, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 588458, 1083, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 589641, 1083, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 590824, 1083, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 592007, 1083, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 593190, 1083, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 594373, 1083, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 595556, 1083, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 596739, 1083, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 597922, 1083, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 599105, 1083, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 600288, 1083, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 601471, 1083, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 602654, 1083, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 603837, 1083, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 605020, 1083, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 606203, 1083, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 607386, 1083, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 608569, 1083, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 609752, 1083, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 610935, 1083, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 612118, 1083, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 613301, 1083, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 614484, 1083, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 615667, 1083, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 616850, 1083, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 618033, 1083, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 619216, 1083, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 620399, 1083, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 621582, 1083, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 622765, 1083, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 623948, 1083, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 625131, 1083, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 626314, 1083, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 627497, 1083, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 628680, 1083, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 629863, 1083, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 631046, 1083, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 632229, 1083, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 633412, 1083, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 634595, 1083, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 635778, 1083, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 636961, 1083, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 638144, 1083, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized1.m new file mode 100644 index 0000000..f3e8395 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized1.m @@ -0,0 +1,120 @@ +% Instantiate simulation from modified knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Author: Bonny Jain, bonny.jain@mit.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SingleGeneOptimized < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGeneOptimized(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + + %% create new genes, transcription units, etc. + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); %normal, cold shock, heat shock + geneA = Gene(kb, NaN, {'GeneA'}, {'Gene A'}, {'genA'}, {''}, {'mRNA'}, 0, {''}, ... + 580177, 1083, true, {''}, meanHL, expression); + + tuA = TranscriptionUnit(kb, NaN, {'TuA'}, {'Transcription unit A'},... + -35, 6, ... + -10, 6, ... + -1); + + monA = ProteinMonomer(kb, NaN, {'MonomerA'}, {'Protein monomer A'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + cpxAA = ProteinComplex(kb, NaN, {'ComplexAA'}, {'Macromolecular complex AA'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCTGTTACTTTATATGATGTTGCTGAATATGCTGGTGTTTCATATCAAACTGTTTCAAGAGTTGTTAATCAAGCTTCACATGTTTCAGCTAAAACTAGAGAAAAAGTTGAAGCTGCTATGGCTGAATTAAATTATATTCCTAATAGAGTTGCTCAACAATTAGCTGGTAAACAATCATTATTAATTGGTGTTGCTACTTCATCATTAGCTTTACATGCTCCTTCACAAATTGTTGCTGCTATTAAATCAAGAGCTGATCAATTAGGTGCTTCAGTTGTTGTTTCAATGGTTGAAAGATCAGGTGTTGAAGCTTGTAAAGCTGCTGTTCATAATTTATTAGCTCAAAGAGTTTCAGGTTTAATTATTAATTATCCTTTAGATGATCAAGATGCTATTGCTGTTGAAGCTGCTTGTACTAATGTTCCTGCTTTATTTTTAGATGTTTCAGATCAAACTCCTATTAATTCAATTATTTTTTCACATGAAGATGGTACTAGATTAGGTGTTGAACATTTAGTTGCTTTAGGTCATCAACAAATTGCTTTATTAGCTGGTCCTTTATCATCAGTTTCAGCTAGATTAAGATTAGCTGGTTGGCATAAATATTTAACTAGAAATCAAATTCAACCTATTGCTGAAAGAGAAGGTGATTGGTCAGCTATGTCAGGTTTTCAACAAACTATGCAAATGTTAAATGAAGGTATTGTTCCTACTGCTATGTTAGTTGCTAATGATCAAATGGCTTTAGGTGCTATGAGAGCTATTACTGAATCAGGTTTAAGAGTTGGTGCTGATATTTCAGTTGTTGGTTATGATGATACTGAAGATTCATCATGTTATATTCCTCCTTCAACTACTATTAAACAAGATTTTAGATTATTAGGTCAAACTTCAGTTGATAGATTATTACAATTATCACAAGGTCAAGCTGTTAAAGGTAATCAATTATTACCTGTTTCATTAGTTAAAAGAAAAACTACTTTAGCTCCTAATACTCAAACTGCTTCACCTAGAGCTTTAGCTGATTCATTAATGCAATTAGCTAGACAAGTTTCAAGATTAGAATCAGGTCAATAA'; + genome.sequence = [genome.sequence promoter lacI]; + genome.sequenceLength = length(genome.sequence); + + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + + %% create new relationships among new genes, transcription units, etc. + geneA.genome = genome; + geneA.transcriptionUnits = tuA; + geneA.proteinMonomers = monA; + geneA.compartment = cytosol; + + tuA.genome = genome; + tuA.genes = geneA; + tuA.geneCompartments = cytosol; + tuA.compartment = cytosol; + + monA.gene = geneA; + monA.geneCompartments = cytosol; + monA.compartment = cytosol; + + cpxAA.proteinMonomers = monA; + cpxAA.proteinMonomerCompartments = cytosol; + cpxAA.proteinMonomerCoefficients = 4; + cpxAA.compartment = cytosol; + cpxAA.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA]; + + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA]; + + %% class super class method + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + + function modifyNetworkParameters(~, sim) + %% get handles + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + + %% get constants + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + + %% get parameter values + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + + %% calculate modified parameter values + %set binding probability of new TUs + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + + %renormalize + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + + %update expression + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + + %% update parameter values + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized10.m new file mode 100644 index 0000000..e6021b0 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized10.m @@ -0,0 +1,482 @@ +% Instantiate simulation from modified knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Author: Bonny Jain, bonny.jain@mit.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SingleGene10Optimized < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene10Optimized(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + + %% create new genes, transcription units, etc. + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); %normal, cold shock, heat shock + + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, ... + 580177, 1083, true, {''}, meanHL, expression); + + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, ... + 581360, 1083, true, {''}, meanHL, expression); + + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, ... + 582543, 1083, true, {''}, meanHL, expression); + + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, ... + 583726, 1083, true, {''}, meanHL, expression); + + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, ... + 584909, 1083, true, {''}, meanHL, expression); + + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, ... + 585092, 1083, true, {''}, meanHL, expression); + + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, ... + 587275, 1083, true, {''}, meanHL, expression); + + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, ... + 588458, 1083, true, {''}, meanHL, expression); + + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, ... + 589641, 1083, true, {''}, meanHL, expression); + + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, ... + 590824, 1083, true, {''}, meanHL, expression); + + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'},... + -35, 6, ... + -10, 6, ... + -1); + + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCTGTTACTTTATATGATGTTGCTGAATATGCTGGTGTTTCATATCAAACTGTTTCAAGAGTTGTTAATCAAGCTTCACATGTTTCAGCTAAAACTAGAGAAAAAGTTGAAGCTGCTATGGCTGAATTAAATTATATTCCTAATAGAGTTGCTCAACAATTAGCTGGTAAACAATCATTATTAATTGGTGTTGCTACTTCATCATTAGCTTTACATGCTCCTTCACAAATTGTTGCTGCTATTAAATCAAGAGCTGATCAATTAGGTGCTTCAGTTGTTGTTTCAATGGTTGAAAGATCAGGTGTTGAAGCTTGTAAAGCTGCTGTTCATAATTTATTAGCTCAAAGAGTTTCAGGTTTAATTATTAATTATCCTTTAGATGATCAAGATGCTATTGCTGTTGAAGCTGCTTGTACTAATGTTCCTGCTTTATTTTTAGATGTTTCAGATCAAACTCCTATTAATTCAATTATTTTTTCACATGAAGATGGTACTAGATTAGGTGTTGAACATTTAGTTGCTTTAGGTCATCAACAAATTGCTTTATTAGCTGGTCCTTTATCATCAGTTTCAGCTAGATTAAGATTAGCTGGTTGGCATAAATATTTAACTAGAAATCAAATTCAACCTATTGCTGAAAGAGAAGGTGATTGGTCAGCTATGTCAGGTTTTCAACAAACTATGCAAATGTTAAATGAAGGTATTGTTCCTACTGCTATGTTAGTTGCTAATGATCAAATGGCTTTAGGTGCTATGAGAGCTATTACTGAATCAGGTTTAAGAGTTGGTGCTGATATTTCAGTTGTTGGTTATGATGATACTGAAGATTCATCATGTTATATTCCTCCTTCAACTACTATTAAACAAGATTTTAGATTATTAGGTCAAACTTCAGTTGATAGATTATTACAATTATCACAAGGTCAAGCTGTTAAAGGTAATCAATTATTACCTGTTTCATTAGTTAAAAGAAAAACTACTTTAGCTCCTAATACTCAAACTGCTTCACCTAGAGCTTTAGCTGATTCATTAATGCAATTAGCTAGACAAGTTTCAAGATTAGAATCAGGTCAATAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + + %% create new relationships among new genes, transcription units, etc. + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + + %% class super class method + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + + function modifyNetworkParameters(~, sim) + %% get handles + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + + %% get constants + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + + %% get parameter values + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + + %% calculate modified parameter values + %set binding probability of new TUs + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + + %renormalize + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + + %update expression + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + + %% update parameter values + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized100.m new file mode 100644 index 0000000..0e55296 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized100.m @@ -0,0 +1,2451 @@ +classdef SingleGene100Optimized < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene100Optimized(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 1083, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581360, 1083, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582543, 1083, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583726, 1083, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584909, 1083, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 586092, 1083, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 587275, 1083, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 588458, 1083, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 589641, 1083, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 590824, 1083, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 592007, 1083, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 593190, 1083, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 594373, 1083, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 595556, 1083, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 596739, 1083, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 597922, 1083, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 599105, 1083, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 600288, 1083, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 601471, 1083, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 602654, 1083, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 603837, 1083, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 605020, 1083, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 606203, 1083, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 607386, 1083, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 608569, 1083, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 609752, 1083, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 610935, 1083, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 612118, 1083, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 613301, 1083, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 614484, 1083, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 615667, 1083, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 616850, 1083, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 618033, 1083, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 619216, 1083, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 620399, 1083, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 621582, 1083, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 622765, 1083, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 623948, 1083, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 625131, 1083, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 626314, 1083, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 627497, 1083, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 628680, 1083, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 629863, 1083, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 631046, 1083, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 632229, 1083, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 633412, 1083, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 634595, 1083, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 635778, 1083, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 636961, 1083, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 638144, 1083, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 639327, 1083, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 640510, 1083, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 641693, 1083, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 642876, 1083, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 644059, 1083, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 645242, 1083, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 646425, 1083, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 647608, 1083, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 648791, 1083, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 649974, 1083, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 651157, 1083, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 652340, 1083, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 653523, 1083, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 654706, 1083, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 655889, 1083, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 657072, 1083, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 658255, 1083, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 659438, 1083, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 660621, 1083, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 661804, 1083, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 662987, 1083, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 664170, 1083, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 665353, 1083, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 666536, 1083, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 667719, 1083, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 668902, 1083, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 670085, 1083, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 671268, 1083, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 672451, 1083, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 673634, 1083, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 674817, 1083, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 676000, 1083, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 677183, 1083, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 678366, 1083, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 679549, 1083, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 680732, 1083, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 681915, 1083, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 683098, 1083, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 684281, 1083, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 685464, 1083, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 686647, 1083, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 687830, 1083, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 689013, 1083, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 690196, 1083, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 691379, 1083, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 692562, 1083, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 693745, 1083, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 694928, 1083, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 696111, 1083, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 697294, 1083, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCTGTTACTTTATATGATGTTGCTGAATATGCTGGTGTTTCATATCAAACTGTTTCAAGAGTTGTTAATCAAGCTTCACATGTTTCAGCTAAAACTAGAGAAAAAGTTGAAGCTGCTATGGCTGAATTAAATTATATTCCTAATAGAGTTGCTCAACAATTAGCTGGTAAACAATCATTATTAATTGGTGTTGCTACTTCATCATTAGCTTTACATGCTCCTTCACAAATTGTTGCTGCTATTAAATCAAGAGCTGATCAATTAGGTGCTTCAGTTGTTGTTTCAATGGTTGAAAGATCAGGTGTTGAAGCTTGTAAAGCTGCTGTTCATAATTTATTAGCTCAAAGAGTTTCAGGTTTAATTATTAATTATCCTTTAGATGATCAAGATGCTATTGCTGTTGAAGCTGCTTGTACTAATGTTCCTGCTTTATTTTTAGATGTTTCAGATCAAACTCCTATTAATTCAATTATTTTTTCACATGAAGATGGTACTAGATTAGGTGTTGAACATTTAGTTGCTTTAGGTCATCAACAAATTGCTTTATTAGCTGGTCCTTTATCATCAGTTTCAGCTAGATTAAGATTAGCTGGTTGGCATAAATATTTAACTAGAAATCAAATTCAACCTATTGCTGAAAGAGAAGGTGATTGGTCAGCTATGTCAGGTTTTCAACAAACTATGCAAATGTTAAATGAAGGTATTGTTCCTACTGCTATGTTAGTTGCTAATGATCAAATGGCTTTAGGTGCTATGAGAGCTATTACTGAATCAGGTTTAAGAGTTGGTGCTGATATTTCAGTTGTTGGTTATGATGATACTGAAGATTCATCATGTTATATTCCTCCTTCAACTACTATTAAACAAGATTTTAGATTATTAGGTCAAACTTCAGTTGATAGATTATTACAATTATCACAAGGTCAAGCTGTTAAAGGTAATCAATTATTACCTGTTTCATTAGTTAAAAGAAAAACTACTTTAGCTCCTAATACTCAAACTGCTTCACCTAGAGCTTTAGCTGATTCATTAATGCAATTAGCTAGACAAGTTTCAAGATTAGAATCAGGTCAATAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized20.m new file mode 100644 index 0000000..825d483 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized20.m @@ -0,0 +1,531 @@ +classdef SingleGene20Optimized < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene20Optimized(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 1083, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581360, 1083, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582543, 1083, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583726, 1083, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584909, 1083, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 586092, 1083, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 587275, 1083, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 588458, 1083, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 589641, 1083, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 590824, 1083, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 592007, 1083, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 593190, 1083, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 594373, 1083, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 595556, 1083, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 596739, 1083, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 597922, 1083, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 599105, 1083, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 600288, 1083, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 601471, 1083, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 602654, 1083, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCTGTTACTTTATATGATGTTGCTGAATATGCTGGTGTTTCATATCAAACTGTTTCAAGAGTTGTTAATCAAGCTTCACATGTTTCAGCTAAAACTAGAGAAAAAGTTGAAGCTGCTATGGCTGAATTAAATTATATTCCTAATAGAGTTGCTCAACAATTAGCTGGTAAACAATCATTATTAATTGGTGTTGCTACTTCATCATTAGCTTTACATGCTCCTTCACAAATTGTTGCTGCTATTAAATCAAGAGCTGATCAATTAGGTGCTTCAGTTGTTGTTTCAATGGTTGAAAGATCAGGTGTTGAAGCTTGTAAAGCTGCTGTTCATAATTTATTAGCTCAAAGAGTTTCAGGTTTAATTATTAATTATCCTTTAGATGATCAAGATGCTATTGCTGTTGAAGCTGCTTGTACTAATGTTCCTGCTTTATTTTTAGATGTTTCAGATCAAACTCCTATTAATTCAATTATTTTTTCACATGAAGATGGTACTAGATTAGGTGTTGAACATTTAGTTGCTTTAGGTCATCAACAAATTGCTTTATTAGCTGGTCCTTTATCATCAGTTTCAGCTAGATTAAGATTAGCTGGTTGGCATAAATATTTAACTAGAAATCAAATTCAACCTATTGCTGAAAGAGAAGGTGATTGGTCAGCTATGTCAGGTTTTCAACAAACTATGCAAATGTTAAATGAAGGTATTGTTCCTACTGCTATGTTAGTTGCTAATGATCAAATGGCTTTAGGTGCTATGAGAGCTATTACTGAATCAGGTTTAAGAGTTGGTGCTGATATTTCAGTTGTTGGTTATGATGATACTGAAGATTCATCATGTTATATTCCTCCTTCAACTACTATTAAACAAGATTTTAGATTATTAGGTCAAACTTCAGTTGATAGATTATTACAATTATCACAAGGTCAAGCTGTTAAAGGTAATCAATTATTACCTGTTTCATTAGTTAAAAGAAAAACTACTTTAGCTCCTAATACTCAAACTGCTTCACCTAGAGCTTTAGCTGATTCATTAATGCAATTAGCTAGACAAGTTTCAAGATTAGAATCAGGTCAATAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA2.gene = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + monA3.gene = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + monA4.gene = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + monA5.gene = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA6.gene = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + monA7.gene = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + monA8.gene = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + monA9.gene = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + monA10.gene = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA11.gene = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + monA12.gene = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + monA13.gene = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + monA14.gene = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + monA15.gene = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + monA16.gene = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + monA17.gene = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + monA18.gene = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + monA19.gene = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + monA20.gene = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({TuA1, TuA2, TuA3, TuA4, TuA5, TuA6, TuA7, TuA8, TuA9, TuA10, TuA11, TuA12, TuA13, TuA14, TuA15, TuA16, TuA17, TuA18, TuA19, TuA20}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized5.m new file mode 100644 index 0000000..251d980 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized5.m @@ -0,0 +1,280 @@ +% Instantiate simulation from modified knowledge base. +% +% Author: Jonathan Karr, jkarr@stanford.edu +% Author: Bonny Jain, bonny.jain@mit.edu +% Affilitation: Covert Lab, Department of Bioengineering, Stanford University +% Last updated: 12/20/2012 +classdef SingleGene5Optimized < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene5Optimized(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + + %% create new genes, transcription units, etc. + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); %normal, cold shock, heat shock + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, ... + 580177, 1083, true, {''}, meanHL, expression); + + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, ... + 581360, 1083, true, {''}, meanHL, expression); + + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, ... + 582543, 1083, true, {''}, meanHL, expression); + + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, ... + 583726, 1083, true, {''}, meanHL, expression); + + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, ... + 584909, 1083, true, {''}, meanHL, expression); + + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'},... + -35, 6, ... + -10, 6, ... + -1); + + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'},... + -35, 6, ... + -10, 6, ... + -1); + + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'},... + {''}, {''}, {''}, ... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + false, {''}, {''}, 0, ... + {''}); + + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'},... + 10, {'dsDNA'}, {'dsDNA'}, ... + {''}, {''}, {''}, {''}, {''}, {''}, ... + {''}, {''}); + + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCTGTTACTTTATATGATGTTGCTGAATATGCTGGTGTTTCATATCAAACTGTTTCAAGAGTTGTTAATCAAGCTTCACATGTTTCAGCTAAAACTAGAGAAAAAGTTGAAGCTGCTATGGCTGAATTAAATTATATTCCTAATAGAGTTGCTCAACAATTAGCTGGTAAACAATCATTATTAATTGGTGTTGCTACTTCATCATTAGCTTTACATGCTCCTTCACAAATTGTTGCTGCTATTAAATCAAGAGCTGATCAATTAGGTGCTTCAGTTGTTGTTTCAATGGTTGAAAGATCAGGTGTTGAAGCTTGTAAAGCTGCTGTTCATAATTTATTAGCTCAAAGAGTTTCAGGTTTAATTATTAATTATCCTTTAGATGATCAAGATGCTATTGCTGTTGAAGCTGCTTGTACTAATGTTCCTGCTTTATTTTTAGATGTTTCAGATCAAACTCCTATTAATTCAATTATTTTTTCACATGAAGATGGTACTAGATTAGGTGTTGAACATTTAGTTGCTTTAGGTCATCAACAAATTGCTTTATTAGCTGGTCCTTTATCATCAGTTTCAGCTAGATTAAGATTAGCTGGTTGGCATAAATATTTAACTAGAAATCAAATTCAACCTATTGCTGAAAGAGAAGGTGATTGGTCAGCTATGTCAGGTTTTCAACAAACTATGCAAATGTTAAATGAAGGTATTGTTCCTACTGCTATGTTAGTTGCTAATGATCAAATGGCTTTAGGTGCTATGAGAGCTATTACTGAATCAGGTTTAAGAGTTGGTGCTGATATTTCAGTTGTTGGTTATGATGATACTGAAGATTCATCATGTTATATTCCTCCTTCAACTACTATTAAACAAGATTTTAGATTATTAGGTCAAACTTCAGTTGATAGATTATTACAATTATCACAAGGTCAAGCTGTTAAAGGTAATCAATTATTACCTGTTTCATTAGTTAAAAGAAAAACTACTTTAGCTCCTAATACTCAAACTGCTTCACCTAGAGCTTTAGCTGATTCATTAATGCAATTAGCTAGACAAGTTTCAAGATTAGAATCAGGTCAATAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + + %% create new relationships among new genes, transcription units, etc. + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + + %% class super class method + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + end + + function modifyNetworkParameters(~, sim) + %% get handles + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + + %% get constants + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + + %% get parameter values + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + + %% calculate modified parameter values + %set binding probability of new TUs + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + + %renormalize + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + + %update expression + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + + %% update parameter values + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized50.m new file mode 100644 index 0000000..6ac44fd --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SinglelacIOptimized50.m @@ -0,0 +1,1251 @@ +classdef SingleGene50Optimized < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingleGene50Optimized(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 1083, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 581360, 1083, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 582543, 1083, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 583726, 1083, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 584909, 1083, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 586092, 1083, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 587275, 1083, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 588458, 1083, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 589641, 1083, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 590824, 1083, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 592007, 1083, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 593190, 1083, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 594373, 1083, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 595556, 1083, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 596739, 1083, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 597922, 1083, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 599105, 1083, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 600288, 1083, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 601471, 1083, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 602654, 1083, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 603837, 1083, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 605020, 1083, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 606203, 1083, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 607386, 1083, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 608569, 1083, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 609752, 1083, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 610935, 1083, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 612118, 1083, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 613301, 1083, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 614484, 1083, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 615667, 1083, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 616850, 1083, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 618033, 1083, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 619216, 1083, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 620399, 1083, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 621582, 1083, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 622765, 1083, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 623948, 1083, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 625131, 1083, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 626314, 1083, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 627497, 1083, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 628680, 1083, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 629863, 1083, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 631046, 1083, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 632229, 1083, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 633412, 1083, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 634595, 1083, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 635778, 1083, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 636961, 1083, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 638144, 1083, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + lacI = 'ATGAAACCTGTTACTTTATATGATGTTGCTGAATATGCTGGTGTTTCATATCAAACTGTTTCAAGAGTTGTTAATCAAGCTTCACATGTTTCAGCTAAAACTAGAGAAAAAGTTGAAGCTGCTATGGCTGAATTAAATTATATTCCTAATAGAGTTGCTCAACAATTAGCTGGTAAACAATCATTATTAATTGGTGTTGCTACTTCATCATTAGCTTTACATGCTCCTTCACAAATTGTTGCTGCTATTAAATCAAGAGCTGATCAATTAGGTGCTTCAGTTGTTGTTTCAATGGTTGAAAGATCAGGTGTTGAAGCTTGTAAAGCTGCTGTTCATAATTTATTAGCTCAAAGAGTTTCAGGTTTAATTATTAATTATCCTTTAGATGATCAAGATGCTATTGCTGTTGAAGCTGCTTGTACTAATGTTCCTGCTTTATTTTTAGATGTTTCAGATCAAACTCCTATTAATTCAATTATTTTTTCACATGAAGATGGTACTAGATTAGGTGTTGAACATTTAGTTGCTTTAGGTCATCAACAAATTGCTTTATTAGCTGGTCCTTTATCATCAGTTTCAGCTAGATTAAGATTAGCTGGTTGGCATAAATATTTAACTAGAAATCAAATTCAACCTATTGCTGAAAGAGAAGGTGATTGGTCAGCTATGTCAGGTTTTCAACAAACTATGCAAATGTTAAATGAAGGTATTGTTCCTACTGCTATGTTAGTTGCTAATGATCAAATGGCTTTAGGTGCTATGAGAGCTATTACTGAATCAGGTTTAAGAGTTGGTGCTGATATTTCAGTTGTTGGTTATGATGATACTGAAGATTCATCATGTTATATTCCTCCTTCAACTACTATTAAACAAGATTTTAGATTATTAGGTCAAACTTCAGTTGATAGATTATTACAATTATCACAAGGTCAAGCTGTTAAAGGTAATCAATTATTACCTGTTTCATTAGTTAAAAGAAAAACTACTTTAGCTCCTAATACTCAAACTGCTTCACCTAGAGCTTTAGCTGATTCATTAATGCAATTAGCTAGACAAGTTTCAAGATTAGAATCAGGTCAATAA'; + genome.sequence = [genome.sequence repmat([promoter lacI], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR1.m new file mode 100644 index 0000000..7a5e849 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR1.m @@ -0,0 +1,75 @@ +classdef SingletetR1 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetR1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCCAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCCTAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR10.m new file mode 100644 index 0000000..5f303b4 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR10.m @@ -0,0 +1,291 @@ +classdef SingletetR10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetR10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCCAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCCTAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR100.m new file mode 100644 index 0000000..73d81e0 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR100.m @@ -0,0 +1,2451 @@ +classdef SingletetR100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetR100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 587417, 624, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 588141, 624, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 588865, 624, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 589589, 624, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 590313, 624, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 591037, 624, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 591761, 624, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 592485, 624, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 593209, 624, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 593933, 624, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 594657, 624, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 595381, 624, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 596105, 624, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 596829, 624, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 597553, 624, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 598277, 624, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 599001, 624, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 599725, 624, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 600449, 624, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 601173, 624, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 601897, 624, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 602621, 624, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 603345, 624, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 604069, 624, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 604793, 624, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 605517, 624, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 606241, 624, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 606965, 624, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 607689, 624, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 608413, 624, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 609137, 624, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 609861, 624, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 610585, 624, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 611309, 624, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 612033, 624, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 612757, 624, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 613481, 624, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 614205, 624, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 614929, 624, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 615653, 624, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 616377, 624, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 617101, 624, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 617825, 624, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 618549, 624, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 619273, 624, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 619997, 624, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 620721, 624, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 621445, 624, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 622169, 624, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 622893, 624, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 623617, 624, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 624341, 624, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 625065, 624, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 625789, 624, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 626513, 624, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 627237, 624, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 627961, 624, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 628685, 624, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 629409, 624, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 630133, 624, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 630857, 624, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 631581, 624, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 632305, 624, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 633029, 624, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 633753, 624, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 634477, 624, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 635201, 624, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 635925, 624, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 636649, 624, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 637373, 624, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 638097, 624, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 638821, 624, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 639545, 624, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 640269, 624, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 640993, 624, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 641717, 624, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 642441, 624, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 643165, 624, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 643889, 624, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 644613, 624, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 645337, 624, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 646061, 624, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 646785, 624, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 647509, 624, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 648233, 624, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 648957, 624, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 649681, 624, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 650405, 624, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 651129, 624, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 651853, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCCAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCCTAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR20.m new file mode 100644 index 0000000..d58b9f1 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR20.m @@ -0,0 +1,531 @@ +classdef SingletetR20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetR20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 587417, 624, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 588141, 624, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 588865, 624, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 589589, 624, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 590313, 624, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 591037, 624, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 591761, 624, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 592485, 624, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 593209, 624, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 593933, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCCAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCCTAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR5.m new file mode 100644 index 0000000..9bb29fc --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR5.m @@ -0,0 +1,171 @@ +classdef SingletetR5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetR5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCCAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCCTAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR50.m new file mode 100644 index 0000000..46abfce --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetR50.m @@ -0,0 +1,1251 @@ +classdef SingletetR50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetR50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 587417, 624, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 588141, 624, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 588865, 624, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 589589, 624, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 590313, 624, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 591037, 624, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 591761, 624, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 592485, 624, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 593209, 624, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 593933, 624, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 594657, 624, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 595381, 624, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 596105, 624, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 596829, 624, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 597553, 624, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 598277, 624, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 599001, 624, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 599725, 624, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 600449, 624, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 601173, 624, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 601897, 624, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 602621, 624, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 603345, 624, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 604069, 624, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 604793, 624, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 605517, 624, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 606241, 624, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 606965, 624, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 607689, 624, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 608413, 624, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 609137, 624, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 609861, 624, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 610585, 624, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 611309, 624, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 612033, 624, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 612757, 624, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 613481, 624, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 614205, 624, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 614929, 624, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 615653, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCCAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCCTAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized1.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized1.m new file mode 100644 index 0000000..d00b912 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized1.m @@ -0,0 +1,75 @@ +classdef SingletetROptimized1 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetROptimized1(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCAAGATTAGATAAATCAAAAGTTATTAATTCAGCTTTAGAATTATTAAATGAAGTTGGTATTGAAGGTTTAACTACTAGAAAATTAGCTCAAAAATTAGGTGTTGAACAACCTACTTTATATTGGCATGTTAAAAATAAAAGAGCTTTATTAGATGCTTTAGCTATTGAAATGTTAGATAGACATCATACTCATTTTTGTCCTTTAGAAGGTGAATCATGGCAAGATTTTTTAAGAAATAATGCTAAATCATTTAGATGTGCTTTATTATCACATAGAGATGGTGCTAAAGTTCATTTAGGTACTAGACCTACTGAAAAACAATATGAAACTTTAGAAAATCAATTAGCTTTTTTATGTCAACAAGGTTTTTCATTAGAAAATGCTTTATATGCTTTATCAGCTGTTGGTCATTTTACTTTAGGTTGTGTTTTAGAAGATCAAGAACATCAAGTTGCTAAAGAAGAAAGAGAAACTCCTACTACTGATTCAATGCCTCCTTTATTAAGACAAGCTATTGAATTATTTGATCATCAAGGTGCTGAACCTGCTTTTTTATTTGGTTTAGAATTAATTATTTGTGGTTTAGAAAAACAATTAAAATGTGAATCAGGTTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 1])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized10.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized10.m new file mode 100644 index 0000000..06de8cd --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized10.m @@ -0,0 +1,291 @@ +classdef SingletetROptimized10 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetROptimized10(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCAAGATTAGATAAATCAAAAGTTATTAATTCAGCTTTAGAATTATTAAATGAAGTTGGTATTGAAGGTTTAACTACTAGAAAATTAGCTCAAAAATTAGGTGTTGAACAACCTACTTTATATTGGCATGTTAAAAATAAAAGAGCTTTATTAGATGCTTTAGCTATTGAAATGTTAGATAGACATCATACTCATTTTTGTCCTTTAGAAGGTGAATCATGGCAAGATTTTTTAAGAAATAATGCTAAATCATTTAGATGTGCTTTATTATCACATAGAGATGGTGCTAAAGTTCATTTAGGTACTAGACCTACTGAAAAACAATATGAAACTTTAGAAAATCAATTAGCTTTTTTATGTCAACAAGGTTTTTCATTAGAAAATGCTTTATATGCTTTATCAGCTGTTGGTCATTTTACTTTAGGTTGTGTTTTAGAAGATCAAGAACATCAAGTTGCTAAAGAAGAAAGAGAAACTCCTACTACTGATTCAATGCCTCCTTTATTAAGACAAGCTATTGAATTATTTGATCATCAAGGTGCTGAACCTGCTTTTTTATTTGGTTTAGAATTAATTATTTGTGGTTTAGAAAAACAATTAAAATGTGAATCAGGTTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 10])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized100.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized100.m new file mode 100644 index 0000000..86fbafa --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized100.m @@ -0,0 +1,2451 @@ +classdef SingletetROptimized100 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetROptimized100(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 587417, 624, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 588141, 624, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 588865, 624, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 589589, 624, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 590313, 624, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 591037, 624, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 591761, 624, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 592485, 624, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 593209, 624, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 593933, 624, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 594657, 624, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 595381, 624, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 596105, 624, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 596829, 624, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 597553, 624, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 598277, 624, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 599001, 624, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 599725, 624, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 600449, 624, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 601173, 624, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 601897, 624, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 602621, 624, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 603345, 624, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 604069, 624, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 604793, 624, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 605517, 624, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 606241, 624, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 606965, 624, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 607689, 624, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 608413, 624, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 609137, 624, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 609861, 624, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 610585, 624, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 611309, 624, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 612033, 624, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 612757, 624, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 613481, 624, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 614205, 624, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 614929, 624, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 615653, 624, true, {''}, meanHL, expression); + geneA51 = Gene(kb, NaN, {'GeneA51'}, {'Gene A51'}, {'genA51'}, {''}, {'mRNA'}, 0, {''}, 616377, 624, true, {''}, meanHL, expression); + geneA52 = Gene(kb, NaN, {'GeneA52'}, {'Gene A52'}, {'genA52'}, {''}, {'mRNA'}, 0, {''}, 617101, 624, true, {''}, meanHL, expression); + geneA53 = Gene(kb, NaN, {'GeneA53'}, {'Gene A53'}, {'genA53'}, {''}, {'mRNA'}, 0, {''}, 617825, 624, true, {''}, meanHL, expression); + geneA54 = Gene(kb, NaN, {'GeneA54'}, {'Gene A54'}, {'genA54'}, {''}, {'mRNA'}, 0, {''}, 618549, 624, true, {''}, meanHL, expression); + geneA55 = Gene(kb, NaN, {'GeneA55'}, {'Gene A55'}, {'genA55'}, {''}, {'mRNA'}, 0, {''}, 619273, 624, true, {''}, meanHL, expression); + geneA56 = Gene(kb, NaN, {'GeneA56'}, {'Gene A56'}, {'genA56'}, {''}, {'mRNA'}, 0, {''}, 619997, 624, true, {''}, meanHL, expression); + geneA57 = Gene(kb, NaN, {'GeneA57'}, {'Gene A57'}, {'genA57'}, {''}, {'mRNA'}, 0, {''}, 620721, 624, true, {''}, meanHL, expression); + geneA58 = Gene(kb, NaN, {'GeneA58'}, {'Gene A58'}, {'genA58'}, {''}, {'mRNA'}, 0, {''}, 621445, 624, true, {''}, meanHL, expression); + geneA59 = Gene(kb, NaN, {'GeneA59'}, {'Gene A59'}, {'genA59'}, {''}, {'mRNA'}, 0, {''}, 622169, 624, true, {''}, meanHL, expression); + geneA60 = Gene(kb, NaN, {'GeneA60'}, {'Gene A60'}, {'genA60'}, {''}, {'mRNA'}, 0, {''}, 622893, 624, true, {''}, meanHL, expression); + geneA61 = Gene(kb, NaN, {'GeneA61'}, {'Gene A61'}, {'genA61'}, {''}, {'mRNA'}, 0, {''}, 623617, 624, true, {''}, meanHL, expression); + geneA62 = Gene(kb, NaN, {'GeneA62'}, {'Gene A62'}, {'genA62'}, {''}, {'mRNA'}, 0, {''}, 624341, 624, true, {''}, meanHL, expression); + geneA63 = Gene(kb, NaN, {'GeneA63'}, {'Gene A63'}, {'genA63'}, {''}, {'mRNA'}, 0, {''}, 625065, 624, true, {''}, meanHL, expression); + geneA64 = Gene(kb, NaN, {'GeneA64'}, {'Gene A64'}, {'genA64'}, {''}, {'mRNA'}, 0, {''}, 625789, 624, true, {''}, meanHL, expression); + geneA65 = Gene(kb, NaN, {'GeneA65'}, {'Gene A65'}, {'genA65'}, {''}, {'mRNA'}, 0, {''}, 626513, 624, true, {''}, meanHL, expression); + geneA66 = Gene(kb, NaN, {'GeneA66'}, {'Gene A66'}, {'genA66'}, {''}, {'mRNA'}, 0, {''}, 627237, 624, true, {''}, meanHL, expression); + geneA67 = Gene(kb, NaN, {'GeneA67'}, {'Gene A67'}, {'genA67'}, {''}, {'mRNA'}, 0, {''}, 627961, 624, true, {''}, meanHL, expression); + geneA68 = Gene(kb, NaN, {'GeneA68'}, {'Gene A68'}, {'genA68'}, {''}, {'mRNA'}, 0, {''}, 628685, 624, true, {''}, meanHL, expression); + geneA69 = Gene(kb, NaN, {'GeneA69'}, {'Gene A69'}, {'genA69'}, {''}, {'mRNA'}, 0, {''}, 629409, 624, true, {''}, meanHL, expression); + geneA70 = Gene(kb, NaN, {'GeneA70'}, {'Gene A70'}, {'genA70'}, {''}, {'mRNA'}, 0, {''}, 630133, 624, true, {''}, meanHL, expression); + geneA71 = Gene(kb, NaN, {'GeneA71'}, {'Gene A71'}, {'genA71'}, {''}, {'mRNA'}, 0, {''}, 630857, 624, true, {''}, meanHL, expression); + geneA72 = Gene(kb, NaN, {'GeneA72'}, {'Gene A72'}, {'genA72'}, {''}, {'mRNA'}, 0, {''}, 631581, 624, true, {''}, meanHL, expression); + geneA73 = Gene(kb, NaN, {'GeneA73'}, {'Gene A73'}, {'genA73'}, {''}, {'mRNA'}, 0, {''}, 632305, 624, true, {''}, meanHL, expression); + geneA74 = Gene(kb, NaN, {'GeneA74'}, {'Gene A74'}, {'genA74'}, {''}, {'mRNA'}, 0, {''}, 633029, 624, true, {''}, meanHL, expression); + geneA75 = Gene(kb, NaN, {'GeneA75'}, {'Gene A75'}, {'genA75'}, {''}, {'mRNA'}, 0, {''}, 633753, 624, true, {''}, meanHL, expression); + geneA76 = Gene(kb, NaN, {'GeneA76'}, {'Gene A76'}, {'genA76'}, {''}, {'mRNA'}, 0, {''}, 634477, 624, true, {''}, meanHL, expression); + geneA77 = Gene(kb, NaN, {'GeneA77'}, {'Gene A77'}, {'genA77'}, {''}, {'mRNA'}, 0, {''}, 635201, 624, true, {''}, meanHL, expression); + geneA78 = Gene(kb, NaN, {'GeneA78'}, {'Gene A78'}, {'genA78'}, {''}, {'mRNA'}, 0, {''}, 635925, 624, true, {''}, meanHL, expression); + geneA79 = Gene(kb, NaN, {'GeneA79'}, {'Gene A79'}, {'genA79'}, {''}, {'mRNA'}, 0, {''}, 636649, 624, true, {''}, meanHL, expression); + geneA80 = Gene(kb, NaN, {'GeneA80'}, {'Gene A80'}, {'genA80'}, {''}, {'mRNA'}, 0, {''}, 637373, 624, true, {''}, meanHL, expression); + geneA81 = Gene(kb, NaN, {'GeneA81'}, {'Gene A81'}, {'genA81'}, {''}, {'mRNA'}, 0, {''}, 638097, 624, true, {''}, meanHL, expression); + geneA82 = Gene(kb, NaN, {'GeneA82'}, {'Gene A82'}, {'genA82'}, {''}, {'mRNA'}, 0, {''}, 638821, 624, true, {''}, meanHL, expression); + geneA83 = Gene(kb, NaN, {'GeneA83'}, {'Gene A83'}, {'genA83'}, {''}, {'mRNA'}, 0, {''}, 639545, 624, true, {''}, meanHL, expression); + geneA84 = Gene(kb, NaN, {'GeneA84'}, {'Gene A84'}, {'genA84'}, {''}, {'mRNA'}, 0, {''}, 640269, 624, true, {''}, meanHL, expression); + geneA85 = Gene(kb, NaN, {'GeneA85'}, {'Gene A85'}, {'genA85'}, {''}, {'mRNA'}, 0, {''}, 640993, 624, true, {''}, meanHL, expression); + geneA86 = Gene(kb, NaN, {'GeneA86'}, {'Gene A86'}, {'genA86'}, {''}, {'mRNA'}, 0, {''}, 641717, 624, true, {''}, meanHL, expression); + geneA87 = Gene(kb, NaN, {'GeneA87'}, {'Gene A87'}, {'genA87'}, {''}, {'mRNA'}, 0, {''}, 642441, 624, true, {''}, meanHL, expression); + geneA88 = Gene(kb, NaN, {'GeneA88'}, {'Gene A88'}, {'genA88'}, {''}, {'mRNA'}, 0, {''}, 643165, 624, true, {''}, meanHL, expression); + geneA89 = Gene(kb, NaN, {'GeneA89'}, {'Gene A89'}, {'genA89'}, {''}, {'mRNA'}, 0, {''}, 643889, 624, true, {''}, meanHL, expression); + geneA90 = Gene(kb, NaN, {'GeneA90'}, {'Gene A90'}, {'genA90'}, {''}, {'mRNA'}, 0, {''}, 644613, 624, true, {''}, meanHL, expression); + geneA91 = Gene(kb, NaN, {'GeneA91'}, {'Gene A91'}, {'genA91'}, {''}, {'mRNA'}, 0, {''}, 645337, 624, true, {''}, meanHL, expression); + geneA92 = Gene(kb, NaN, {'GeneA92'}, {'Gene A92'}, {'genA92'}, {''}, {'mRNA'}, 0, {''}, 646061, 624, true, {''}, meanHL, expression); + geneA93 = Gene(kb, NaN, {'GeneA93'}, {'Gene A93'}, {'genA93'}, {''}, {'mRNA'}, 0, {''}, 646785, 624, true, {''}, meanHL, expression); + geneA94 = Gene(kb, NaN, {'GeneA94'}, {'Gene A94'}, {'genA94'}, {''}, {'mRNA'}, 0, {''}, 647509, 624, true, {''}, meanHL, expression); + geneA95 = Gene(kb, NaN, {'GeneA95'}, {'Gene A95'}, {'genA95'}, {''}, {'mRNA'}, 0, {''}, 648233, 624, true, {''}, meanHL, expression); + geneA96 = Gene(kb, NaN, {'GeneA96'}, {'Gene A96'}, {'genA96'}, {''}, {'mRNA'}, 0, {''}, 648957, 624, true, {''}, meanHL, expression); + geneA97 = Gene(kb, NaN, {'GeneA97'}, {'Gene A97'}, {'genA97'}, {''}, {'mRNA'}, 0, {''}, 649681, 624, true, {''}, meanHL, expression); + geneA98 = Gene(kb, NaN, {'GeneA98'}, {'Gene A98'}, {'genA98'}, {''}, {'mRNA'}, 0, {''}, 650405, 624, true, {''}, meanHL, expression); + geneA99 = Gene(kb, NaN, {'GeneA99'}, {'Gene A99'}, {'genA99'}, {''}, {'mRNA'}, 0, {''}, 651129, 624, true, {''}, meanHL, expression); + geneA100 = Gene(kb, NaN, {'GeneA100'}, {'Gene A100'}, {'genA100'}, {''}, {'mRNA'}, 0, {''}, 651853, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + tuA51 = TranscriptionUnit(kb, NaN, {'TuA51'}, {'Transcription unit A51'}, -35, 6, -35, 6, -1); + tuA52 = TranscriptionUnit(kb, NaN, {'TuA52'}, {'Transcription unit A52'}, -35, 6, -35, 6, -1); + tuA53 = TranscriptionUnit(kb, NaN, {'TuA53'}, {'Transcription unit A53'}, -35, 6, -35, 6, -1); + tuA54 = TranscriptionUnit(kb, NaN, {'TuA54'}, {'Transcription unit A54'}, -35, 6, -35, 6, -1); + tuA55 = TranscriptionUnit(kb, NaN, {'TuA55'}, {'Transcription unit A55'}, -35, 6, -35, 6, -1); + tuA56 = TranscriptionUnit(kb, NaN, {'TuA56'}, {'Transcription unit A56'}, -35, 6, -35, 6, -1); + tuA57 = TranscriptionUnit(kb, NaN, {'TuA57'}, {'Transcription unit A57'}, -35, 6, -35, 6, -1); + tuA58 = TranscriptionUnit(kb, NaN, {'TuA58'}, {'Transcription unit A58'}, -35, 6, -35, 6, -1); + tuA59 = TranscriptionUnit(kb, NaN, {'TuA59'}, {'Transcription unit A59'}, -35, 6, -35, 6, -1); + tuA60 = TranscriptionUnit(kb, NaN, {'TuA60'}, {'Transcription unit A60'}, -35, 6, -35, 6, -1); + tuA61 = TranscriptionUnit(kb, NaN, {'TuA61'}, {'Transcription unit A61'}, -35, 6, -35, 6, -1); + tuA62 = TranscriptionUnit(kb, NaN, {'TuA62'}, {'Transcription unit A62'}, -35, 6, -35, 6, -1); + tuA63 = TranscriptionUnit(kb, NaN, {'TuA63'}, {'Transcription unit A63'}, -35, 6, -35, 6, -1); + tuA64 = TranscriptionUnit(kb, NaN, {'TuA64'}, {'Transcription unit A64'}, -35, 6, -35, 6, -1); + tuA65 = TranscriptionUnit(kb, NaN, {'TuA65'}, {'Transcription unit A65'}, -35, 6, -35, 6, -1); + tuA66 = TranscriptionUnit(kb, NaN, {'TuA66'}, {'Transcription unit A66'}, -35, 6, -35, 6, -1); + tuA67 = TranscriptionUnit(kb, NaN, {'TuA67'}, {'Transcription unit A67'}, -35, 6, -35, 6, -1); + tuA68 = TranscriptionUnit(kb, NaN, {'TuA68'}, {'Transcription unit A68'}, -35, 6, -35, 6, -1); + tuA69 = TranscriptionUnit(kb, NaN, {'TuA69'}, {'Transcription unit A69'}, -35, 6, -35, 6, -1); + tuA70 = TranscriptionUnit(kb, NaN, {'TuA70'}, {'Transcription unit A70'}, -35, 6, -35, 6, -1); + tuA71 = TranscriptionUnit(kb, NaN, {'TuA71'}, {'Transcription unit A71'}, -35, 6, -35, 6, -1); + tuA72 = TranscriptionUnit(kb, NaN, {'TuA72'}, {'Transcription unit A72'}, -35, 6, -35, 6, -1); + tuA73 = TranscriptionUnit(kb, NaN, {'TuA73'}, {'Transcription unit A73'}, -35, 6, -35, 6, -1); + tuA74 = TranscriptionUnit(kb, NaN, {'TuA74'}, {'Transcription unit A74'}, -35, 6, -35, 6, -1); + tuA75 = TranscriptionUnit(kb, NaN, {'TuA75'}, {'Transcription unit A75'}, -35, 6, -35, 6, -1); + tuA76 = TranscriptionUnit(kb, NaN, {'TuA76'}, {'Transcription unit A76'}, -35, 6, -35, 6, -1); + tuA77 = TranscriptionUnit(kb, NaN, {'TuA77'}, {'Transcription unit A77'}, -35, 6, -35, 6, -1); + tuA78 = TranscriptionUnit(kb, NaN, {'TuA78'}, {'Transcription unit A78'}, -35, 6, -35, 6, -1); + tuA79 = TranscriptionUnit(kb, NaN, {'TuA79'}, {'Transcription unit A79'}, -35, 6, -35, 6, -1); + tuA80 = TranscriptionUnit(kb, NaN, {'TuA80'}, {'Transcription unit A80'}, -35, 6, -35, 6, -1); + tuA81 = TranscriptionUnit(kb, NaN, {'TuA81'}, {'Transcription unit A81'}, -35, 6, -35, 6, -1); + tuA82 = TranscriptionUnit(kb, NaN, {'TuA82'}, {'Transcription unit A82'}, -35, 6, -35, 6, -1); + tuA83 = TranscriptionUnit(kb, NaN, {'TuA83'}, {'Transcription unit A83'}, -35, 6, -35, 6, -1); + tuA84 = TranscriptionUnit(kb, NaN, {'TuA84'}, {'Transcription unit A84'}, -35, 6, -35, 6, -1); + tuA85 = TranscriptionUnit(kb, NaN, {'TuA85'}, {'Transcription unit A85'}, -35, 6, -35, 6, -1); + tuA86 = TranscriptionUnit(kb, NaN, {'TuA86'}, {'Transcription unit A86'}, -35, 6, -35, 6, -1); + tuA87 = TranscriptionUnit(kb, NaN, {'TuA87'}, {'Transcription unit A87'}, -35, 6, -35, 6, -1); + tuA88 = TranscriptionUnit(kb, NaN, {'TuA88'}, {'Transcription unit A88'}, -35, 6, -35, 6, -1); + tuA89 = TranscriptionUnit(kb, NaN, {'TuA89'}, {'Transcription unit A89'}, -35, 6, -35, 6, -1); + tuA90 = TranscriptionUnit(kb, NaN, {'TuA90'}, {'Transcription unit A90'}, -35, 6, -35, 6, -1); + tuA91 = TranscriptionUnit(kb, NaN, {'TuA91'}, {'Transcription unit A91'}, -35, 6, -35, 6, -1); + tuA92 = TranscriptionUnit(kb, NaN, {'TuA92'}, {'Transcription unit A92'}, -35, 6, -35, 6, -1); + tuA93 = TranscriptionUnit(kb, NaN, {'TuA93'}, {'Transcription unit A93'}, -35, 6, -35, 6, -1); + tuA94 = TranscriptionUnit(kb, NaN, {'TuA94'}, {'Transcription unit A94'}, -35, 6, -35, 6, -1); + tuA95 = TranscriptionUnit(kb, NaN, {'TuA95'}, {'Transcription unit A95'}, -35, 6, -35, 6, -1); + tuA96 = TranscriptionUnit(kb, NaN, {'TuA96'}, {'Transcription unit A96'}, -35, 6, -35, 6, -1); + tuA97 = TranscriptionUnit(kb, NaN, {'TuA97'}, {'Transcription unit A97'}, -35, 6, -35, 6, -1); + tuA98 = TranscriptionUnit(kb, NaN, {'TuA98'}, {'Transcription unit A98'}, -35, 6, -35, 6, -1); + tuA99 = TranscriptionUnit(kb, NaN, {'TuA99'}, {'Transcription unit A99'}, -35, 6, -35, 6, -1); + tuA100 = TranscriptionUnit(kb, NaN, {'TuA100'}, {'Transcription unit A100'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA51 = ProteinMonomer(kb, NaN, {'MonomerA51'}, {'Protein monomer A51'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA52 = ProteinMonomer(kb, NaN, {'MonomerA52'}, {'Protein monomer A52'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA53 = ProteinMonomer(kb, NaN, {'MonomerA53'}, {'Protein monomer A53'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA54 = ProteinMonomer(kb, NaN, {'MonomerA54'}, {'Protein monomer A54'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA55 = ProteinMonomer(kb, NaN, {'MonomerA55'}, {'Protein monomer A55'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA56 = ProteinMonomer(kb, NaN, {'MonomerA56'}, {'Protein monomer A56'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA57 = ProteinMonomer(kb, NaN, {'MonomerA57'}, {'Protein monomer A57'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA58 = ProteinMonomer(kb, NaN, {'MonomerA58'}, {'Protein monomer A58'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA59 = ProteinMonomer(kb, NaN, {'MonomerA59'}, {'Protein monomer A59'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA60 = ProteinMonomer(kb, NaN, {'MonomerA60'}, {'Protein monomer A60'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA61 = ProteinMonomer(kb, NaN, {'MonomerA61'}, {'Protein monomer A61'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA62 = ProteinMonomer(kb, NaN, {'MonomerA62'}, {'Protein monomer A62'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA63 = ProteinMonomer(kb, NaN, {'MonomerA63'}, {'Protein monomer A63'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA64 = ProteinMonomer(kb, NaN, {'MonomerA64'}, {'Protein monomer A64'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA65 = ProteinMonomer(kb, NaN, {'MonomerA65'}, {'Protein monomer A65'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA66 = ProteinMonomer(kb, NaN, {'MonomerA66'}, {'Protein monomer A66'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA67 = ProteinMonomer(kb, NaN, {'MonomerA67'}, {'Protein monomer A67'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA68 = ProteinMonomer(kb, NaN, {'MonomerA68'}, {'Protein monomer A68'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA69 = ProteinMonomer(kb, NaN, {'MonomerA69'}, {'Protein monomer A69'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA70 = ProteinMonomer(kb, NaN, {'MonomerA70'}, {'Protein monomer A70'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA71 = ProteinMonomer(kb, NaN, {'MonomerA71'}, {'Protein monomer A71'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA72 = ProteinMonomer(kb, NaN, {'MonomerA72'}, {'Protein monomer A72'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA73 = ProteinMonomer(kb, NaN, {'MonomerA73'}, {'Protein monomer A73'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA74 = ProteinMonomer(kb, NaN, {'MonomerA74'}, {'Protein monomer A74'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA75 = ProteinMonomer(kb, NaN, {'MonomerA75'}, {'Protein monomer A75'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA76 = ProteinMonomer(kb, NaN, {'MonomerA76'}, {'Protein monomer A76'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA77 = ProteinMonomer(kb, NaN, {'MonomerA77'}, {'Protein monomer A77'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA78 = ProteinMonomer(kb, NaN, {'MonomerA78'}, {'Protein monomer A78'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA79 = ProteinMonomer(kb, NaN, {'MonomerA79'}, {'Protein monomer A79'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA80 = ProteinMonomer(kb, NaN, {'MonomerA80'}, {'Protein monomer A80'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA81 = ProteinMonomer(kb, NaN, {'MonomerA81'}, {'Protein monomer A81'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA82 = ProteinMonomer(kb, NaN, {'MonomerA82'}, {'Protein monomer A82'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA83 = ProteinMonomer(kb, NaN, {'MonomerA83'}, {'Protein monomer A83'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA84 = ProteinMonomer(kb, NaN, {'MonomerA84'}, {'Protein monomer A84'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA85 = ProteinMonomer(kb, NaN, {'MonomerA85'}, {'Protein monomer A85'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA86 = ProteinMonomer(kb, NaN, {'MonomerA86'}, {'Protein monomer A86'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA87 = ProteinMonomer(kb, NaN, {'MonomerA87'}, {'Protein monomer A87'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA88 = ProteinMonomer(kb, NaN, {'MonomerA88'}, {'Protein monomer A88'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA89 = ProteinMonomer(kb, NaN, {'MonomerA89'}, {'Protein monomer A89'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA90 = ProteinMonomer(kb, NaN, {'MonomerA90'}, {'Protein monomer A90'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA91 = ProteinMonomer(kb, NaN, {'MonomerA91'}, {'Protein monomer A91'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA92 = ProteinMonomer(kb, NaN, {'MonomerA92'}, {'Protein monomer A92'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA93 = ProteinMonomer(kb, NaN, {'MonomerA93'}, {'Protein monomer A93'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA94 = ProteinMonomer(kb, NaN, {'MonomerA94'}, {'Protein monomer A94'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA95 = ProteinMonomer(kb, NaN, {'MonomerA95'}, {'Protein monomer A95'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA96 = ProteinMonomer(kb, NaN, {'MonomerA96'}, {'Protein monomer A96'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA97 = ProteinMonomer(kb, NaN, {'MonomerA97'}, {'Protein monomer A97'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA98 = ProteinMonomer(kb, NaN, {'MonomerA98'}, {'Protein monomer A98'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA99 = ProteinMonomer(kb, NaN, {'MonomerA99'}, {'Protein monomer A99'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA100 = ProteinMonomer(kb, NaN, {'MonomerA100'}, {'Protein monomer A100'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA51 = ProteinComplex(kb, NaN, {'ComplexAA51'}, {'Macromolecular complex AA51'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA52 = ProteinComplex(kb, NaN, {'ComplexAA52'}, {'Macromolecular complex AA52'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA53 = ProteinComplex(kb, NaN, {'ComplexAA53'}, {'Macromolecular complex AA53'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA54 = ProteinComplex(kb, NaN, {'ComplexAA54'}, {'Macromolecular complex AA54'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA55 = ProteinComplex(kb, NaN, {'ComplexAA55'}, {'Macromolecular complex AA55'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA56 = ProteinComplex(kb, NaN, {'ComplexAA56'}, {'Macromolecular complex AA56'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA57 = ProteinComplex(kb, NaN, {'ComplexAA57'}, {'Macromolecular complex AA57'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA58 = ProteinComplex(kb, NaN, {'ComplexAA58'}, {'Macromolecular complex AA58'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA59 = ProteinComplex(kb, NaN, {'ComplexAA59'}, {'Macromolecular complex AA59'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA60 = ProteinComplex(kb, NaN, {'ComplexAA60'}, {'Macromolecular complex AA60'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA61 = ProteinComplex(kb, NaN, {'ComplexAA61'}, {'Macromolecular complex AA61'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA62 = ProteinComplex(kb, NaN, {'ComplexAA62'}, {'Macromolecular complex AA62'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA63 = ProteinComplex(kb, NaN, {'ComplexAA63'}, {'Macromolecular complex AA63'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA64 = ProteinComplex(kb, NaN, {'ComplexAA64'}, {'Macromolecular complex AA64'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA65 = ProteinComplex(kb, NaN, {'ComplexAA65'}, {'Macromolecular complex AA65'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA66 = ProteinComplex(kb, NaN, {'ComplexAA66'}, {'Macromolecular complex AA66'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA67 = ProteinComplex(kb, NaN, {'ComplexAA67'}, {'Macromolecular complex AA67'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA68 = ProteinComplex(kb, NaN, {'ComplexAA68'}, {'Macromolecular complex AA68'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA69 = ProteinComplex(kb, NaN, {'ComplexAA69'}, {'Macromolecular complex AA69'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA70 = ProteinComplex(kb, NaN, {'ComplexAA70'}, {'Macromolecular complex AA70'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA71 = ProteinComplex(kb, NaN, {'ComplexAA71'}, {'Macromolecular complex AA71'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA72 = ProteinComplex(kb, NaN, {'ComplexAA72'}, {'Macromolecular complex AA72'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA73 = ProteinComplex(kb, NaN, {'ComplexAA73'}, {'Macromolecular complex AA73'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA74 = ProteinComplex(kb, NaN, {'ComplexAA74'}, {'Macromolecular complex AA74'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA75 = ProteinComplex(kb, NaN, {'ComplexAA75'}, {'Macromolecular complex AA75'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA76 = ProteinComplex(kb, NaN, {'ComplexAA76'}, {'Macromolecular complex AA76'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA77 = ProteinComplex(kb, NaN, {'ComplexAA77'}, {'Macromolecular complex AA77'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA78 = ProteinComplex(kb, NaN, {'ComplexAA78'}, {'Macromolecular complex AA78'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA79 = ProteinComplex(kb, NaN, {'ComplexAA79'}, {'Macromolecular complex AA79'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA80 = ProteinComplex(kb, NaN, {'ComplexAA80'}, {'Macromolecular complex AA80'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA81 = ProteinComplex(kb, NaN, {'ComplexAA81'}, {'Macromolecular complex AA81'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA82 = ProteinComplex(kb, NaN, {'ComplexAA82'}, {'Macromolecular complex AA82'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA83 = ProteinComplex(kb, NaN, {'ComplexAA83'}, {'Macromolecular complex AA83'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA84 = ProteinComplex(kb, NaN, {'ComplexAA84'}, {'Macromolecular complex AA84'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA85 = ProteinComplex(kb, NaN, {'ComplexAA85'}, {'Macromolecular complex AA85'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA86 = ProteinComplex(kb, NaN, {'ComplexAA86'}, {'Macromolecular complex AA86'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA87 = ProteinComplex(kb, NaN, {'ComplexAA87'}, {'Macromolecular complex AA87'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA88 = ProteinComplex(kb, NaN, {'ComplexAA88'}, {'Macromolecular complex AA88'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA89 = ProteinComplex(kb, NaN, {'ComplexAA89'}, {'Macromolecular complex AA89'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA90 = ProteinComplex(kb, NaN, {'ComplexAA90'}, {'Macromolecular complex AA90'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA91 = ProteinComplex(kb, NaN, {'ComplexAA91'}, {'Macromolecular complex AA91'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA92 = ProteinComplex(kb, NaN, {'ComplexAA92'}, {'Macromolecular complex AA92'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA93 = ProteinComplex(kb, NaN, {'ComplexAA93'}, {'Macromolecular complex AA93'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA94 = ProteinComplex(kb, NaN, {'ComplexAA94'}, {'Macromolecular complex AA94'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA95 = ProteinComplex(kb, NaN, {'ComplexAA95'}, {'Macromolecular complex AA95'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA96 = ProteinComplex(kb, NaN, {'ComplexAA96'}, {'Macromolecular complex AA96'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA97 = ProteinComplex(kb, NaN, {'ComplexAA97'}, {'Macromolecular complex AA97'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA98 = ProteinComplex(kb, NaN, {'ComplexAA98'}, {'Macromolecular complex AA98'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA99 = ProteinComplex(kb, NaN, {'ComplexAA99'}, {'Macromolecular complex AA99'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA100 = ProteinComplex(kb, NaN, {'ComplexAA100'}, {'Macromolecular complex AA100'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCAAGATTAGATAAATCAAAAGTTATTAATTCAGCTTTAGAATTATTAAATGAAGTTGGTATTGAAGGTTTAACTACTAGAAAATTAGCTCAAAAATTAGGTGTTGAACAACCTACTTTATATTGGCATGTTAAAAATAAAAGAGCTTTATTAGATGCTTTAGCTATTGAAATGTTAGATAGACATCATACTCATTTTTGTCCTTTAGAAGGTGAATCATGGCAAGATTTTTTAAGAAATAATGCTAAATCATTTAGATGTGCTTTATTATCACATAGAGATGGTGCTAAAGTTCATTTAGGTACTAGACCTACTGAAAAACAATATGAAACTTTAGAAAATCAATTAGCTTTTTTATGTCAACAAGGTTTTTCATTAGAAAATGCTTTATATGCTTTATCAGCTGTTGGTCATTTTACTTTAGGTTGTGTTTTAGAAGATCAAGAACATCAAGTTGCTAAAGAAGAAAGAGAAACTCCTACTACTGATTCAATGCCTCCTTTATTAAGACAAGCTATTGAATTATTTGATCATCAAGGTGCTGAACCTGCTTTTTTATTTGGTTTAGAATTAATTATTTGTGGTTTAGAAAAACAATTAAAATGTGAATCAGGTTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 100])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + geneA51.genome = genome; + geneA51.transcriptionUnits = tuA51; + geneA51.proteinMonomers = monA51; + geneA51.compartment = cytosol; + + geneA52.genome = genome; + geneA52.transcriptionUnits = tuA52; + geneA52.proteinMonomers = monA52; + geneA52.compartment = cytosol; + + geneA53.genome = genome; + geneA53.transcriptionUnits = tuA53; + geneA53.proteinMonomers = monA53; + geneA53.compartment = cytosol; + + geneA54.genome = genome; + geneA54.transcriptionUnits = tuA54; + geneA54.proteinMonomers = monA54; + geneA54.compartment = cytosol; + + geneA55.genome = genome; + geneA55.transcriptionUnits = tuA55; + geneA55.proteinMonomers = monA55; + geneA55.compartment = cytosol; + + geneA56.genome = genome; + geneA56.transcriptionUnits = tuA56; + geneA56.proteinMonomers = monA56; + geneA56.compartment = cytosol; + + geneA57.genome = genome; + geneA57.transcriptionUnits = tuA57; + geneA57.proteinMonomers = monA57; + geneA57.compartment = cytosol; + + geneA58.genome = genome; + geneA58.transcriptionUnits = tuA58; + geneA58.proteinMonomers = monA58; + geneA58.compartment = cytosol; + + geneA59.genome = genome; + geneA59.transcriptionUnits = tuA59; + geneA59.proteinMonomers = monA59; + geneA59.compartment = cytosol; + + geneA60.genome = genome; + geneA60.transcriptionUnits = tuA60; + geneA60.proteinMonomers = monA60; + geneA60.compartment = cytosol; + + geneA61.genome = genome; + geneA61.transcriptionUnits = tuA61; + geneA61.proteinMonomers = monA61; + geneA61.compartment = cytosol; + + geneA62.genome = genome; + geneA62.transcriptionUnits = tuA62; + geneA62.proteinMonomers = monA62; + geneA62.compartment = cytosol; + + geneA63.genome = genome; + geneA63.transcriptionUnits = tuA63; + geneA63.proteinMonomers = monA63; + geneA63.compartment = cytosol; + + geneA64.genome = genome; + geneA64.transcriptionUnits = tuA64; + geneA64.proteinMonomers = monA64; + geneA64.compartment = cytosol; + + geneA65.genome = genome; + geneA65.transcriptionUnits = tuA65; + geneA65.proteinMonomers = monA65; + geneA65.compartment = cytosol; + + geneA66.genome = genome; + geneA66.transcriptionUnits = tuA66; + geneA66.proteinMonomers = monA66; + geneA66.compartment = cytosol; + + geneA67.genome = genome; + geneA67.transcriptionUnits = tuA67; + geneA67.proteinMonomers = monA67; + geneA67.compartment = cytosol; + + geneA68.genome = genome; + geneA68.transcriptionUnits = tuA68; + geneA68.proteinMonomers = monA68; + geneA68.compartment = cytosol; + + geneA69.genome = genome; + geneA69.transcriptionUnits = tuA69; + geneA69.proteinMonomers = monA69; + geneA69.compartment = cytosol; + + geneA70.genome = genome; + geneA70.transcriptionUnits = tuA70; + geneA70.proteinMonomers = monA70; + geneA70.compartment = cytosol; + + geneA71.genome = genome; + geneA71.transcriptionUnits = tuA71; + geneA71.proteinMonomers = monA71; + geneA71.compartment = cytosol; + + geneA72.genome = genome; + geneA72.transcriptionUnits = tuA72; + geneA72.proteinMonomers = monA72; + geneA72.compartment = cytosol; + + geneA73.genome = genome; + geneA73.transcriptionUnits = tuA73; + geneA73.proteinMonomers = monA73; + geneA73.compartment = cytosol; + + geneA74.genome = genome; + geneA74.transcriptionUnits = tuA74; + geneA74.proteinMonomers = monA74; + geneA74.compartment = cytosol; + + geneA75.genome = genome; + geneA75.transcriptionUnits = tuA75; + geneA75.proteinMonomers = monA75; + geneA75.compartment = cytosol; + + geneA76.genome = genome; + geneA76.transcriptionUnits = tuA76; + geneA76.proteinMonomers = monA76; + geneA76.compartment = cytosol; + + geneA77.genome = genome; + geneA77.transcriptionUnits = tuA77; + geneA77.proteinMonomers = monA77; + geneA77.compartment = cytosol; + + geneA78.genome = genome; + geneA78.transcriptionUnits = tuA78; + geneA78.proteinMonomers = monA78; + geneA78.compartment = cytosol; + + geneA79.genome = genome; + geneA79.transcriptionUnits = tuA79; + geneA79.proteinMonomers = monA79; + geneA79.compartment = cytosol; + + geneA80.genome = genome; + geneA80.transcriptionUnits = tuA80; + geneA80.proteinMonomers = monA80; + geneA80.compartment = cytosol; + + geneA81.genome = genome; + geneA81.transcriptionUnits = tuA81; + geneA81.proteinMonomers = monA81; + geneA81.compartment = cytosol; + + geneA82.genome = genome; + geneA82.transcriptionUnits = tuA82; + geneA82.proteinMonomers = monA82; + geneA82.compartment = cytosol; + + geneA83.genome = genome; + geneA83.transcriptionUnits = tuA83; + geneA83.proteinMonomers = monA83; + geneA83.compartment = cytosol; + + geneA84.genome = genome; + geneA84.transcriptionUnits = tuA84; + geneA84.proteinMonomers = monA84; + geneA84.compartment = cytosol; + + geneA85.genome = genome; + geneA85.transcriptionUnits = tuA85; + geneA85.proteinMonomers = monA85; + geneA85.compartment = cytosol; + + geneA86.genome = genome; + geneA86.transcriptionUnits = tuA86; + geneA86.proteinMonomers = monA86; + geneA86.compartment = cytosol; + + geneA87.genome = genome; + geneA87.transcriptionUnits = tuA87; + geneA87.proteinMonomers = monA87; + geneA87.compartment = cytosol; + + geneA88.genome = genome; + geneA88.transcriptionUnits = tuA88; + geneA88.proteinMonomers = monA88; + geneA88.compartment = cytosol; + + geneA89.genome = genome; + geneA89.transcriptionUnits = tuA89; + geneA89.proteinMonomers = monA89; + geneA89.compartment = cytosol; + + geneA90.genome = genome; + geneA90.transcriptionUnits = tuA90; + geneA90.proteinMonomers = monA90; + geneA90.compartment = cytosol; + + geneA91.genome = genome; + geneA91.transcriptionUnits = tuA91; + geneA91.proteinMonomers = monA91; + geneA91.compartment = cytosol; + + geneA92.genome = genome; + geneA92.transcriptionUnits = tuA92; + geneA92.proteinMonomers = monA92; + geneA92.compartment = cytosol; + + geneA93.genome = genome; + geneA93.transcriptionUnits = tuA93; + geneA93.proteinMonomers = monA93; + geneA93.compartment = cytosol; + + geneA94.genome = genome; + geneA94.transcriptionUnits = tuA94; + geneA94.proteinMonomers = monA94; + geneA94.compartment = cytosol; + + geneA95.genome = genome; + geneA95.transcriptionUnits = tuA95; + geneA95.proteinMonomers = monA95; + geneA95.compartment = cytosol; + + geneA96.genome = genome; + geneA96.transcriptionUnits = tuA96; + geneA96.proteinMonomers = monA96; + geneA96.compartment = cytosol; + + geneA97.genome = genome; + geneA97.transcriptionUnits = tuA97; + geneA97.proteinMonomers = monA97; + geneA97.compartment = cytosol; + + geneA98.genome = genome; + geneA98.transcriptionUnits = tuA98; + geneA98.proteinMonomers = monA98; + geneA98.compartment = cytosol; + + geneA99.genome = genome; + geneA99.transcriptionUnits = tuA99; + geneA99.proteinMonomers = monA99; + geneA99.compartment = cytosol; + + geneA100.genome = genome; + geneA100.transcriptionUnits = tuA100; + geneA100.proteinMonomers = monA100; + geneA100.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + tuA51.genome = genome; + tuA51.genes = geneA51; + tuA51.geneCompartments = cytosol; + tuA51.compartment = cytosol; + + tuA52.genome = genome; + tuA52.genes = geneA52; + tuA52.geneCompartments = cytosol; + tuA52.compartment = cytosol; + + tuA53.genome = genome; + tuA53.genes = geneA53; + tuA53.geneCompartments = cytosol; + tuA53.compartment = cytosol; + + tuA54.genome = genome; + tuA54.genes = geneA54; + tuA54.geneCompartments = cytosol; + tuA54.compartment = cytosol; + + tuA55.genome = genome; + tuA55.genes = geneA55; + tuA55.geneCompartments = cytosol; + tuA55.compartment = cytosol; + + tuA56.genome = genome; + tuA56.genes = geneA56; + tuA56.geneCompartments = cytosol; + tuA56.compartment = cytosol; + + tuA57.genome = genome; + tuA57.genes = geneA57; + tuA57.geneCompartments = cytosol; + tuA57.compartment = cytosol; + + tuA58.genome = genome; + tuA58.genes = geneA58; + tuA58.geneCompartments = cytosol; + tuA58.compartment = cytosol; + + tuA59.genome = genome; + tuA59.genes = geneA59; + tuA59.geneCompartments = cytosol; + tuA59.compartment = cytosol; + + tuA60.genome = genome; + tuA60.genes = geneA60; + tuA60.geneCompartments = cytosol; + tuA60.compartment = cytosol; + + tuA61.genome = genome; + tuA61.genes = geneA61; + tuA61.geneCompartments = cytosol; + tuA61.compartment = cytosol; + + tuA62.genome = genome; + tuA62.genes = geneA62; + tuA62.geneCompartments = cytosol; + tuA62.compartment = cytosol; + + tuA63.genome = genome; + tuA63.genes = geneA63; + tuA63.geneCompartments = cytosol; + tuA63.compartment = cytosol; + + tuA64.genome = genome; + tuA64.genes = geneA64; + tuA64.geneCompartments = cytosol; + tuA64.compartment = cytosol; + + tuA65.genome = genome; + tuA65.genes = geneA65; + tuA65.geneCompartments = cytosol; + tuA65.compartment = cytosol; + + tuA66.genome = genome; + tuA66.genes = geneA66; + tuA66.geneCompartments = cytosol; + tuA66.compartment = cytosol; + + tuA67.genome = genome; + tuA67.genes = geneA67; + tuA67.geneCompartments = cytosol; + tuA67.compartment = cytosol; + + tuA68.genome = genome; + tuA68.genes = geneA68; + tuA68.geneCompartments = cytosol; + tuA68.compartment = cytosol; + + tuA69.genome = genome; + tuA69.genes = geneA69; + tuA69.geneCompartments = cytosol; + tuA69.compartment = cytosol; + + tuA70.genome = genome; + tuA70.genes = geneA70; + tuA70.geneCompartments = cytosol; + tuA70.compartment = cytosol; + + tuA71.genome = genome; + tuA71.genes = geneA71; + tuA71.geneCompartments = cytosol; + tuA71.compartment = cytosol; + + tuA72.genome = genome; + tuA72.genes = geneA72; + tuA72.geneCompartments = cytosol; + tuA72.compartment = cytosol; + + tuA73.genome = genome; + tuA73.genes = geneA73; + tuA73.geneCompartments = cytosol; + tuA73.compartment = cytosol; + + tuA74.genome = genome; + tuA74.genes = geneA74; + tuA74.geneCompartments = cytosol; + tuA74.compartment = cytosol; + + tuA75.genome = genome; + tuA75.genes = geneA75; + tuA75.geneCompartments = cytosol; + tuA75.compartment = cytosol; + + tuA76.genome = genome; + tuA76.genes = geneA76; + tuA76.geneCompartments = cytosol; + tuA76.compartment = cytosol; + + tuA77.genome = genome; + tuA77.genes = geneA77; + tuA77.geneCompartments = cytosol; + tuA77.compartment = cytosol; + + tuA78.genome = genome; + tuA78.genes = geneA78; + tuA78.geneCompartments = cytosol; + tuA78.compartment = cytosol; + + tuA79.genome = genome; + tuA79.genes = geneA79; + tuA79.geneCompartments = cytosol; + tuA79.compartment = cytosol; + + tuA80.genome = genome; + tuA80.genes = geneA80; + tuA80.geneCompartments = cytosol; + tuA80.compartment = cytosol; + + tuA81.genome = genome; + tuA81.genes = geneA81; + tuA81.geneCompartments = cytosol; + tuA81.compartment = cytosol; + + tuA82.genome = genome; + tuA82.genes = geneA82; + tuA82.geneCompartments = cytosol; + tuA82.compartment = cytosol; + + tuA83.genome = genome; + tuA83.genes = geneA83; + tuA83.geneCompartments = cytosol; + tuA83.compartment = cytosol; + + tuA84.genome = genome; + tuA84.genes = geneA84; + tuA84.geneCompartments = cytosol; + tuA84.compartment = cytosol; + + tuA85.genome = genome; + tuA85.genes = geneA85; + tuA85.geneCompartments = cytosol; + tuA85.compartment = cytosol; + + tuA86.genome = genome; + tuA86.genes = geneA86; + tuA86.geneCompartments = cytosol; + tuA86.compartment = cytosol; + + tuA87.genome = genome; + tuA87.genes = geneA87; + tuA87.geneCompartments = cytosol; + tuA87.compartment = cytosol; + + tuA88.genome = genome; + tuA88.genes = geneA88; + tuA88.geneCompartments = cytosol; + tuA88.compartment = cytosol; + + tuA89.genome = genome; + tuA89.genes = geneA89; + tuA89.geneCompartments = cytosol; + tuA89.compartment = cytosol; + + tuA90.genome = genome; + tuA90.genes = geneA90; + tuA90.geneCompartments = cytosol; + tuA90.compartment = cytosol; + + tuA91.genome = genome; + tuA91.genes = geneA91; + tuA91.geneCompartments = cytosol; + tuA91.compartment = cytosol; + + tuA92.genome = genome; + tuA92.genes = geneA92; + tuA92.geneCompartments = cytosol; + tuA92.compartment = cytosol; + + tuA93.genome = genome; + tuA93.genes = geneA93; + tuA93.geneCompartments = cytosol; + tuA93.compartment = cytosol; + + tuA94.genome = genome; + tuA94.genes = geneA94; + tuA94.geneCompartments = cytosol; + tuA94.compartment = cytosol; + + tuA95.genome = genome; + tuA95.genes = geneA95; + tuA95.geneCompartments = cytosol; + tuA95.compartment = cytosol; + + tuA96.genome = genome; + tuA96.genes = geneA96; + tuA96.geneCompartments = cytosol; + tuA96.compartment = cytosol; + + tuA97.genome = genome; + tuA97.genes = geneA97; + tuA97.geneCompartments = cytosol; + tuA97.compartment = cytosol; + + tuA98.genome = genome; + tuA98.genes = geneA98; + tuA98.geneCompartments = cytosol; + tuA98.compartment = cytosol; + + tuA99.genome = genome; + tuA99.genes = geneA99; + tuA99.geneCompartments = cytosol; + tuA99.compartment = cytosol; + + tuA100.genome = genome; + tuA100.genes = geneA100; + tuA100.geneCompartments = cytosol; + tuA100.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + monA51.gene = geneA51; + monA51.geneCompartments = cytosol; + monA51.compartment = cytosol; + + monA52.gene = geneA52; + monA52.geneCompartments = cytosol; + monA52.compartment = cytosol; + + monA53.gene = geneA53; + monA53.geneCompartments = cytosol; + monA53.compartment = cytosol; + + monA54.gene = geneA54; + monA54.geneCompartments = cytosol; + monA54.compartment = cytosol; + + monA55.gene = geneA55; + monA55.geneCompartments = cytosol; + monA55.compartment = cytosol; + + monA56.gene = geneA56; + monA56.geneCompartments = cytosol; + monA56.compartment = cytosol; + + monA57.gene = geneA57; + monA57.geneCompartments = cytosol; + monA57.compartment = cytosol; + + monA58.gene = geneA58; + monA58.geneCompartments = cytosol; + monA58.compartment = cytosol; + + monA59.gene = geneA59; + monA59.geneCompartments = cytosol; + monA59.compartment = cytosol; + + monA60.gene = geneA60; + monA60.geneCompartments = cytosol; + monA60.compartment = cytosol; + + monA61.gene = geneA61; + monA61.geneCompartments = cytosol; + monA61.compartment = cytosol; + + monA62.gene = geneA62; + monA62.geneCompartments = cytosol; + monA62.compartment = cytosol; + + monA63.gene = geneA63; + monA63.geneCompartments = cytosol; + monA63.compartment = cytosol; + + monA64.gene = geneA64; + monA64.geneCompartments = cytosol; + monA64.compartment = cytosol; + + monA65.gene = geneA65; + monA65.geneCompartments = cytosol; + monA65.compartment = cytosol; + + monA66.gene = geneA66; + monA66.geneCompartments = cytosol; + monA66.compartment = cytosol; + + monA67.gene = geneA67; + monA67.geneCompartments = cytosol; + monA67.compartment = cytosol; + + monA68.gene = geneA68; + monA68.geneCompartments = cytosol; + monA68.compartment = cytosol; + + monA69.gene = geneA69; + monA69.geneCompartments = cytosol; + monA69.compartment = cytosol; + + monA70.gene = geneA70; + monA70.geneCompartments = cytosol; + monA70.compartment = cytosol; + + monA71.gene = geneA71; + monA71.geneCompartments = cytosol; + monA71.compartment = cytosol; + + monA72.gene = geneA72; + monA72.geneCompartments = cytosol; + monA72.compartment = cytosol; + + monA73.gene = geneA73; + monA73.geneCompartments = cytosol; + monA73.compartment = cytosol; + + monA74.gene = geneA74; + monA74.geneCompartments = cytosol; + monA74.compartment = cytosol; + + monA75.gene = geneA75; + monA75.geneCompartments = cytosol; + monA75.compartment = cytosol; + + monA76.gene = geneA76; + monA76.geneCompartments = cytosol; + monA76.compartment = cytosol; + + monA77.gene = geneA77; + monA77.geneCompartments = cytosol; + monA77.compartment = cytosol; + + monA78.gene = geneA78; + monA78.geneCompartments = cytosol; + monA78.compartment = cytosol; + + monA79.gene = geneA79; + monA79.geneCompartments = cytosol; + monA79.compartment = cytosol; + + monA80.gene = geneA80; + monA80.geneCompartments = cytosol; + monA80.compartment = cytosol; + + monA81.gene = geneA81; + monA81.geneCompartments = cytosol; + monA81.compartment = cytosol; + + monA82.gene = geneA82; + monA82.geneCompartments = cytosol; + monA82.compartment = cytosol; + + monA83.gene = geneA83; + monA83.geneCompartments = cytosol; + monA83.compartment = cytosol; + + monA84.gene = geneA84; + monA84.geneCompartments = cytosol; + monA84.compartment = cytosol; + + monA85.gene = geneA85; + monA85.geneCompartments = cytosol; + monA85.compartment = cytosol; + + monA86.gene = geneA86; + monA86.geneCompartments = cytosol; + monA86.compartment = cytosol; + + monA87.gene = geneA87; + monA87.geneCompartments = cytosol; + monA87.compartment = cytosol; + + monA88.gene = geneA88; + monA88.geneCompartments = cytosol; + monA88.compartment = cytosol; + + monA89.gene = geneA89; + monA89.geneCompartments = cytosol; + monA89.compartment = cytosol; + + monA90.gene = geneA90; + monA90.geneCompartments = cytosol; + monA90.compartment = cytosol; + + monA91.gene = geneA91; + monA91.geneCompartments = cytosol; + monA91.compartment = cytosol; + + monA92.gene = geneA92; + monA92.geneCompartments = cytosol; + monA92.compartment = cytosol; + + monA93.gene = geneA93; + monA93.geneCompartments = cytosol; + monA93.compartment = cytosol; + + monA94.gene = geneA94; + monA94.geneCompartments = cytosol; + monA94.compartment = cytosol; + + monA95.gene = geneA95; + monA95.geneCompartments = cytosol; + monA95.compartment = cytosol; + + monA96.gene = geneA96; + monA96.geneCompartments = cytosol; + monA96.compartment = cytosol; + + monA97.gene = geneA97; + monA97.geneCompartments = cytosol; + monA97.compartment = cytosol; + + monA98.gene = geneA98; + monA98.geneCompartments = cytosol; + monA98.compartment = cytosol; + + monA99.gene = geneA99; + monA99.geneCompartments = cytosol; + monA99.compartment = cytosol; + + monA100.gene = geneA100; + monA100.geneCompartments = cytosol; + monA100.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA51.proteinMonomers = monA51; + cpxAA51.proteinMonomerCompartments = cytosol; + cpxAA51.proteinMonomerCoefficients = 4; + cpxAA51.compartment = cytosol; + cpxAA51.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA52.proteinMonomers = monA52; + cpxAA52.proteinMonomerCompartments = cytosol; + cpxAA52.proteinMonomerCoefficients = 4; + cpxAA52.compartment = cytosol; + cpxAA52.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA53.proteinMonomers = monA53; + cpxAA53.proteinMonomerCompartments = cytosol; + cpxAA53.proteinMonomerCoefficients = 4; + cpxAA53.compartment = cytosol; + cpxAA53.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA54.proteinMonomers = monA54; + cpxAA54.proteinMonomerCompartments = cytosol; + cpxAA54.proteinMonomerCoefficients = 4; + cpxAA54.compartment = cytosol; + cpxAA54.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA55.proteinMonomers = monA55; + cpxAA55.proteinMonomerCompartments = cytosol; + cpxAA55.proteinMonomerCoefficients = 4; + cpxAA55.compartment = cytosol; + cpxAA55.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA56.proteinMonomers = monA56; + cpxAA56.proteinMonomerCompartments = cytosol; + cpxAA56.proteinMonomerCoefficients = 4; + cpxAA56.compartment = cytosol; + cpxAA56.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA57.proteinMonomers = monA57; + cpxAA57.proteinMonomerCompartments = cytosol; + cpxAA57.proteinMonomerCoefficients = 4; + cpxAA57.compartment = cytosol; + cpxAA57.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA58.proteinMonomers = monA58; + cpxAA58.proteinMonomerCompartments = cytosol; + cpxAA58.proteinMonomerCoefficients = 4; + cpxAA58.compartment = cytosol; + cpxAA58.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA59.proteinMonomers = monA59; + cpxAA59.proteinMonomerCompartments = cytosol; + cpxAA59.proteinMonomerCoefficients = 4; + cpxAA59.compartment = cytosol; + cpxAA59.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA60.proteinMonomers = monA60; + cpxAA60.proteinMonomerCompartments = cytosol; + cpxAA60.proteinMonomerCoefficients = 4; + cpxAA60.compartment = cytosol; + cpxAA60.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA61.proteinMonomers = monA61; + cpxAA61.proteinMonomerCompartments = cytosol; + cpxAA61.proteinMonomerCoefficients = 4; + cpxAA61.compartment = cytosol; + cpxAA61.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA62.proteinMonomers = monA62; + cpxAA62.proteinMonomerCompartments = cytosol; + cpxAA62.proteinMonomerCoefficients = 4; + cpxAA62.compartment = cytosol; + cpxAA62.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA63.proteinMonomers = monA63; + cpxAA63.proteinMonomerCompartments = cytosol; + cpxAA63.proteinMonomerCoefficients = 4; + cpxAA63.compartment = cytosol; + cpxAA63.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA64.proteinMonomers = monA64; + cpxAA64.proteinMonomerCompartments = cytosol; + cpxAA64.proteinMonomerCoefficients = 4; + cpxAA64.compartment = cytosol; + cpxAA64.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA65.proteinMonomers = monA65; + cpxAA65.proteinMonomerCompartments = cytosol; + cpxAA65.proteinMonomerCoefficients = 4; + cpxAA65.compartment = cytosol; + cpxAA65.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA66.proteinMonomers = monA66; + cpxAA66.proteinMonomerCompartments = cytosol; + cpxAA66.proteinMonomerCoefficients = 4; + cpxAA66.compartment = cytosol; + cpxAA66.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA67.proteinMonomers = monA67; + cpxAA67.proteinMonomerCompartments = cytosol; + cpxAA67.proteinMonomerCoefficients = 4; + cpxAA67.compartment = cytosol; + cpxAA67.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA68.proteinMonomers = monA68; + cpxAA68.proteinMonomerCompartments = cytosol; + cpxAA68.proteinMonomerCoefficients = 4; + cpxAA68.compartment = cytosol; + cpxAA68.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA69.proteinMonomers = monA69; + cpxAA69.proteinMonomerCompartments = cytosol; + cpxAA69.proteinMonomerCoefficients = 4; + cpxAA69.compartment = cytosol; + cpxAA69.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA70.proteinMonomers = monA70; + cpxAA70.proteinMonomerCompartments = cytosol; + cpxAA70.proteinMonomerCoefficients = 4; + cpxAA70.compartment = cytosol; + cpxAA70.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA71.proteinMonomers = monA71; + cpxAA71.proteinMonomerCompartments = cytosol; + cpxAA71.proteinMonomerCoefficients = 4; + cpxAA71.compartment = cytosol; + cpxAA71.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA72.proteinMonomers = monA72; + cpxAA72.proteinMonomerCompartments = cytosol; + cpxAA72.proteinMonomerCoefficients = 4; + cpxAA72.compartment = cytosol; + cpxAA72.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA73.proteinMonomers = monA73; + cpxAA73.proteinMonomerCompartments = cytosol; + cpxAA73.proteinMonomerCoefficients = 4; + cpxAA73.compartment = cytosol; + cpxAA73.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA74.proteinMonomers = monA74; + cpxAA74.proteinMonomerCompartments = cytosol; + cpxAA74.proteinMonomerCoefficients = 4; + cpxAA74.compartment = cytosol; + cpxAA74.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA75.proteinMonomers = monA75; + cpxAA75.proteinMonomerCompartments = cytosol; + cpxAA75.proteinMonomerCoefficients = 4; + cpxAA75.compartment = cytosol; + cpxAA75.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA76.proteinMonomers = monA76; + cpxAA76.proteinMonomerCompartments = cytosol; + cpxAA76.proteinMonomerCoefficients = 4; + cpxAA76.compartment = cytosol; + cpxAA76.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA77.proteinMonomers = monA77; + cpxAA77.proteinMonomerCompartments = cytosol; + cpxAA77.proteinMonomerCoefficients = 4; + cpxAA77.compartment = cytosol; + cpxAA77.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA78.proteinMonomers = monA78; + cpxAA78.proteinMonomerCompartments = cytosol; + cpxAA78.proteinMonomerCoefficients = 4; + cpxAA78.compartment = cytosol; + cpxAA78.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA79.proteinMonomers = monA79; + cpxAA79.proteinMonomerCompartments = cytosol; + cpxAA79.proteinMonomerCoefficients = 4; + cpxAA79.compartment = cytosol; + cpxAA79.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA80.proteinMonomers = monA80; + cpxAA80.proteinMonomerCompartments = cytosol; + cpxAA80.proteinMonomerCoefficients = 4; + cpxAA80.compartment = cytosol; + cpxAA80.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA81.proteinMonomers = monA81; + cpxAA81.proteinMonomerCompartments = cytosol; + cpxAA81.proteinMonomerCoefficients = 4; + cpxAA81.compartment = cytosol; + cpxAA81.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA82.proteinMonomers = monA82; + cpxAA82.proteinMonomerCompartments = cytosol; + cpxAA82.proteinMonomerCoefficients = 4; + cpxAA82.compartment = cytosol; + cpxAA82.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA83.proteinMonomers = monA83; + cpxAA83.proteinMonomerCompartments = cytosol; + cpxAA83.proteinMonomerCoefficients = 4; + cpxAA83.compartment = cytosol; + cpxAA83.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA84.proteinMonomers = monA84; + cpxAA84.proteinMonomerCompartments = cytosol; + cpxAA84.proteinMonomerCoefficients = 4; + cpxAA84.compartment = cytosol; + cpxAA84.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA85.proteinMonomers = monA85; + cpxAA85.proteinMonomerCompartments = cytosol; + cpxAA85.proteinMonomerCoefficients = 4; + cpxAA85.compartment = cytosol; + cpxAA85.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA86.proteinMonomers = monA86; + cpxAA86.proteinMonomerCompartments = cytosol; + cpxAA86.proteinMonomerCoefficients = 4; + cpxAA86.compartment = cytosol; + cpxAA86.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA87.proteinMonomers = monA87; + cpxAA87.proteinMonomerCompartments = cytosol; + cpxAA87.proteinMonomerCoefficients = 4; + cpxAA87.compartment = cytosol; + cpxAA87.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA88.proteinMonomers = monA88; + cpxAA88.proteinMonomerCompartments = cytosol; + cpxAA88.proteinMonomerCoefficients = 4; + cpxAA88.compartment = cytosol; + cpxAA88.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA89.proteinMonomers = monA89; + cpxAA89.proteinMonomerCompartments = cytosol; + cpxAA89.proteinMonomerCoefficients = 4; + cpxAA89.compartment = cytosol; + cpxAA89.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA90.proteinMonomers = monA90; + cpxAA90.proteinMonomerCompartments = cytosol; + cpxAA90.proteinMonomerCoefficients = 4; + cpxAA90.compartment = cytosol; + cpxAA90.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA91.proteinMonomers = monA91; + cpxAA91.proteinMonomerCompartments = cytosol; + cpxAA91.proteinMonomerCoefficients = 4; + cpxAA91.compartment = cytosol; + cpxAA91.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA92.proteinMonomers = monA92; + cpxAA92.proteinMonomerCompartments = cytosol; + cpxAA92.proteinMonomerCoefficients = 4; + cpxAA92.compartment = cytosol; + cpxAA92.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA93.proteinMonomers = monA93; + cpxAA93.proteinMonomerCompartments = cytosol; + cpxAA93.proteinMonomerCoefficients = 4; + cpxAA93.compartment = cytosol; + cpxAA93.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA94.proteinMonomers = monA94; + cpxAA94.proteinMonomerCompartments = cytosol; + cpxAA94.proteinMonomerCoefficients = 4; + cpxAA94.compartment = cytosol; + cpxAA94.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA95.proteinMonomers = monA95; + cpxAA95.proteinMonomerCompartments = cytosol; + cpxAA95.proteinMonomerCoefficients = 4; + cpxAA95.compartment = cytosol; + cpxAA95.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA96.proteinMonomers = monA96; + cpxAA96.proteinMonomerCompartments = cytosol; + cpxAA96.proteinMonomerCoefficients = 4; + cpxAA96.compartment = cytosol; + cpxAA96.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA97.proteinMonomers = monA97; + cpxAA97.proteinMonomerCompartments = cytosol; + cpxAA97.proteinMonomerCoefficients = 4; + cpxAA97.compartment = cytosol; + cpxAA97.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA98.proteinMonomers = monA98; + cpxAA98.proteinMonomerCompartments = cytosol; + cpxAA98.proteinMonomerCoefficients = 4; + cpxAA98.compartment = cytosol; + cpxAA98.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA99.proteinMonomers = monA99; + cpxAA99.proteinMonomerCompartments = cytosol; + cpxAA99.proteinMonomerCoefficients = 4; + cpxAA99.compartment = cytosol; + cpxAA99.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA100.proteinMonomers = monA100; + cpxAA100.proteinMonomerCompartments = cytosol; + cpxAA100.proteinMonomerCoefficients = 4; + cpxAA100.compartment = cytosol; + cpxAA100.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50; geneA51; geneA52; geneA53; geneA54; geneA55; geneA56; geneA57; geneA58; geneA59; geneA60; geneA61; geneA62; geneA63; geneA64; geneA65; geneA66; geneA67; geneA68; geneA69; geneA70; geneA71; geneA72; geneA73; geneA74; geneA75; geneA76; geneA77; geneA78; geneA79; geneA80; geneA81; geneA82; geneA83; geneA84; geneA85; geneA86; geneA87; geneA88; geneA89; geneA90; geneA91; geneA92; geneA93; geneA94; geneA95; geneA96; geneA97; geneA98; geneA99; geneA100]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50; tuA51; tuA52; tuA53; tuA54; tuA55; tuA56; tuA57; tuA58; tuA59; tuA60; tuA61; tuA62; tuA63; tuA64; tuA65; tuA66; tuA67; tuA68; tuA69; tuA70; tuA71; tuA72; tuA73; tuA74; tuA75; tuA76; tuA77; tuA78; tuA79; tuA80; tuA81; tuA82; tuA83; tuA84; tuA85; tuA86; tuA87; tuA88; tuA89; tuA90; tuA91; tuA92; tuA93; tuA94; tuA95; tuA96; tuA97; tuA98; tuA99; tuA100]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50; monA51; monA52; monA53; monA54; monA55; monA56; monA57; monA58; monA59; monA60; monA61; monA62; monA63; monA64; monA65; monA66; monA67; monA68; monA69; monA70; monA71; monA72; monA73; monA74; monA75; monA76; monA77; monA78; monA79; monA80; monA81; monA82; monA83; monA84; monA85; monA86; monA87; monA88; monA89; monA90; monA91; monA92; monA93; monA94; monA95; monA96; monA97; monA98; monA99; monA100]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50; cpxAA51; cpxAA52; cpxAA53; cpxAA54; cpxAA55; cpxAA56; cpxAA57; cpxAA58; cpxAA59; cpxAA60; cpxAA61; cpxAA62; cpxAA63; cpxAA64; cpxAA65; cpxAA66; cpxAA67; cpxAA68; cpxAA69; cpxAA70; cpxAA71; cpxAA72; cpxAA73; cpxAA74; cpxAA75; cpxAA76; cpxAA77; cpxAA78; cpxAA79; cpxAA80; cpxAA81; cpxAA82; cpxAA83; cpxAA84; cpxAA85; cpxAA86; cpxAA87; cpxAA88; cpxAA89; cpxAA90; cpxAA91; cpxAA92; cpxAA93; cpxAA94; cpxAA95; cpxAA96; cpxAA97; cpxAA98; cpxAA99; cpxAA100]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50', 'TuA51', 'TuA52', 'TuA53', 'TuA54', 'TuA55', 'TuA56', 'TuA57', 'TuA58', 'TuA59', 'TuA60', 'TuA61', 'TuA62', 'TuA63', 'TuA64', 'TuA65', 'TuA66', 'TuA67', 'TuA68', 'TuA69', 'TuA70', 'TuA71', 'TuA72', 'TuA73', 'TuA74', 'TuA75', 'TuA76', 'TuA77', 'TuA78', 'TuA79', 'TuA80', 'TuA81', 'TuA82', 'TuA83', 'TuA84', 'TuA85', 'TuA86', 'TuA87', 'TuA88', 'TuA89', 'TuA90', 'TuA91', 'TuA92', 'TuA93', 'TuA94', 'TuA95', 'TuA96', 'TuA97', 'TuA98', 'TuA99', 'TuA100'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized20.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized20.m new file mode 100644 index 0000000..b78836e --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized20.m @@ -0,0 +1,531 @@ +classdef SingletetROptimized20 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetROptimized20(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 587417, 624, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 588141, 624, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 588865, 624, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 589589, 624, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 590313, 624, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 591037, 624, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 591761, 624, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 592485, 624, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 593209, 624, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 593933, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCAAGATTAGATAAATCAAAAGTTATTAATTCAGCTTTAGAATTATTAAATGAAGTTGGTATTGAAGGTTTAACTACTAGAAAATTAGCTCAAAAATTAGGTGTTGAACAACCTACTTTATATTGGCATGTTAAAAATAAAAGAGCTTTATTAGATGCTTTAGCTATTGAAATGTTAGATAGACATCATACTCATTTTTGTCCTTTAGAAGGTGAATCATGGCAAGATTTTTTAAGAAATAATGCTAAATCATTTAGATGTGCTTTATTATCACATAGAGATGGTGCTAAAGTTCATTTAGGTACTAGACCTACTGAAAAACAATATGAAACTTTAGAAAATCAATTAGCTTTTTTATGTCAACAAGGTTTTTCATTAGAAAATGCTTTATATGCTTTATCAGCTGTTGGTCATTTTACTTTAGGTTGTGTTTTAGAAGATCAAGAACATCAAGTTGCTAAAGAAGAAAGAGAAACTCCTACTACTGATTCAATGCCTCCTTTATTAAGACAAGCTATTGAATTATTTGATCATCAAGGTGCTGAACCTGCTTTTTTATTTGGTTTAGAATTAATTATTTGTGGTTTAGAAAAACAATTAAAATGTGAATCAGGTTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 20])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized5.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized5.m new file mode 100644 index 0000000..41365a8 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized5.m @@ -0,0 +1,171 @@ +classdef SingletetROptimized5 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetROptimized5(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCAAGATTAGATAAATCAAAAGTTATTAATTCAGCTTTAGAATTATTAAATGAAGTTGGTATTGAAGGTTTAACTACTAGAAAATTAGCTCAAAAATTAGGTGTTGAACAACCTACTTTATATTGGCATGTTAAAAATAAAAGAGCTTTATTAGATGCTTTAGCTATTGAAATGTTAGATAGACATCATACTCATTTTTGTCCTTTAGAAGGTGAATCATGGCAAGATTTTTTAAGAAATAATGCTAAATCATTTAGATGTGCTTTATTATCACATAGAGATGGTGCTAAAGTTCATTTAGGTACTAGACCTACTGAAAAACAATATGAAACTTTAGAAAATCAATTAGCTTTTTTATGTCAACAAGGTTTTTCATTAGAAAATGCTTTATATGCTTTATCAGCTGTTGGTCATTTTACTTTAGGTTGTGTTTTAGAAGATCAAGAACATCAAGTTGCTAAAGAAGAAAGAGAAACTCCTACTACTGATTCAATGCCTCCTTTATTAAGACAAGCTATTGAATTATTTGATCATCAAGGTGCTGAACCTGCTTTTTTATTTGGTTTAGAATTAATTATTTGTGGTTTAGAAAAACAATTAAAATGTGAATCAGGTTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 5])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized50.m b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized50.m new file mode 100644 index 0000000..62726b6 --- /dev/null +++ b/src/+edu/+stanford/+covert/+cell/+sim/+runners/SingletetROptimized50.m @@ -0,0 +1,1251 @@ +classdef SingletetROptimized50 < edu.stanford.covert.cell.sim.runners.SimulationRunner + methods + function this = SingletetROptimized50(varargin) + this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:}); + end + end + + methods (Access = protected) + function modifyNetworkStructure(this, kb) + import edu.stanford.covert.cell.kb.Gene; + import edu.stanford.covert.cell.kb.ProteinMonomer; + import edu.stanford.covert.cell.kb.ProteinComplex; + import edu.stanford.covert.cell.kb.Stimuli; + import edu.stanford.covert.cell.kb.TranscriptionUnit; + meanHL = mean([kb.mRNAGenes.halfLife]); + expression = zeros(1, 3); + geneA1 = Gene(kb, NaN, {'GeneA1'}, {'Gene A1'}, {'genA1'}, {''}, {'mRNA'}, 0, {''}, 580177, 624, true, {''}, meanHL, expression); + geneA2 = Gene(kb, NaN, {'GeneA2'}, {'Gene A2'}, {'genA2'}, {''}, {'mRNA'}, 0, {''}, 580901, 624, true, {''}, meanHL, expression); + geneA3 = Gene(kb, NaN, {'GeneA3'}, {'Gene A3'}, {'genA3'}, {''}, {'mRNA'}, 0, {''}, 581625, 624, true, {''}, meanHL, expression); + geneA4 = Gene(kb, NaN, {'GeneA4'}, {'Gene A4'}, {'genA4'}, {''}, {'mRNA'}, 0, {''}, 582349, 624, true, {''}, meanHL, expression); + geneA5 = Gene(kb, NaN, {'GeneA5'}, {'Gene A5'}, {'genA5'}, {''}, {'mRNA'}, 0, {''}, 583073, 624, true, {''}, meanHL, expression); + geneA6 = Gene(kb, NaN, {'GeneA6'}, {'Gene A6'}, {'genA6'}, {''}, {'mRNA'}, 0, {''}, 583797, 624, true, {''}, meanHL, expression); + geneA7 = Gene(kb, NaN, {'GeneA7'}, {'Gene A7'}, {'genA7'}, {''}, {'mRNA'}, 0, {''}, 584521, 624, true, {''}, meanHL, expression); + geneA8 = Gene(kb, NaN, {'GeneA8'}, {'Gene A8'}, {'genA8'}, {''}, {'mRNA'}, 0, {''}, 585245, 624, true, {''}, meanHL, expression); + geneA9 = Gene(kb, NaN, {'GeneA9'}, {'Gene A9'}, {'genA9'}, {''}, {'mRNA'}, 0, {''}, 585969, 624, true, {''}, meanHL, expression); + geneA10 = Gene(kb, NaN, {'GeneA10'}, {'Gene A10'}, {'genA10'}, {''}, {'mRNA'}, 0, {''}, 586693, 624, true, {''}, meanHL, expression); + geneA11 = Gene(kb, NaN, {'GeneA11'}, {'Gene A11'}, {'genA11'}, {''}, {'mRNA'}, 0, {''}, 587417, 624, true, {''}, meanHL, expression); + geneA12 = Gene(kb, NaN, {'GeneA12'}, {'Gene A12'}, {'genA12'}, {''}, {'mRNA'}, 0, {''}, 588141, 624, true, {''}, meanHL, expression); + geneA13 = Gene(kb, NaN, {'GeneA13'}, {'Gene A13'}, {'genA13'}, {''}, {'mRNA'}, 0, {''}, 588865, 624, true, {''}, meanHL, expression); + geneA14 = Gene(kb, NaN, {'GeneA14'}, {'Gene A14'}, {'genA14'}, {''}, {'mRNA'}, 0, {''}, 589589, 624, true, {''}, meanHL, expression); + geneA15 = Gene(kb, NaN, {'GeneA15'}, {'Gene A15'}, {'genA15'}, {''}, {'mRNA'}, 0, {''}, 590313, 624, true, {''}, meanHL, expression); + geneA16 = Gene(kb, NaN, {'GeneA16'}, {'Gene A16'}, {'genA16'}, {''}, {'mRNA'}, 0, {''}, 591037, 624, true, {''}, meanHL, expression); + geneA17 = Gene(kb, NaN, {'GeneA17'}, {'Gene A17'}, {'genA17'}, {''}, {'mRNA'}, 0, {''}, 591761, 624, true, {''}, meanHL, expression); + geneA18 = Gene(kb, NaN, {'GeneA18'}, {'Gene A18'}, {'genA18'}, {''}, {'mRNA'}, 0, {''}, 592485, 624, true, {''}, meanHL, expression); + geneA19 = Gene(kb, NaN, {'GeneA19'}, {'Gene A19'}, {'genA19'}, {''}, {'mRNA'}, 0, {''}, 593209, 624, true, {''}, meanHL, expression); + geneA20 = Gene(kb, NaN, {'GeneA20'}, {'Gene A20'}, {'genA20'}, {''}, {'mRNA'}, 0, {''}, 593933, 624, true, {''}, meanHL, expression); + geneA21 = Gene(kb, NaN, {'GeneA21'}, {'Gene A21'}, {'genA21'}, {''}, {'mRNA'}, 0, {''}, 594657, 624, true, {''}, meanHL, expression); + geneA22 = Gene(kb, NaN, {'GeneA22'}, {'Gene A22'}, {'genA22'}, {''}, {'mRNA'}, 0, {''}, 595381, 624, true, {''}, meanHL, expression); + geneA23 = Gene(kb, NaN, {'GeneA23'}, {'Gene A23'}, {'genA23'}, {''}, {'mRNA'}, 0, {''}, 596105, 624, true, {''}, meanHL, expression); + geneA24 = Gene(kb, NaN, {'GeneA24'}, {'Gene A24'}, {'genA24'}, {''}, {'mRNA'}, 0, {''}, 596829, 624, true, {''}, meanHL, expression); + geneA25 = Gene(kb, NaN, {'GeneA25'}, {'Gene A25'}, {'genA25'}, {''}, {'mRNA'}, 0, {''}, 597553, 624, true, {''}, meanHL, expression); + geneA26 = Gene(kb, NaN, {'GeneA26'}, {'Gene A26'}, {'genA26'}, {''}, {'mRNA'}, 0, {''}, 598277, 624, true, {''}, meanHL, expression); + geneA27 = Gene(kb, NaN, {'GeneA27'}, {'Gene A27'}, {'genA27'}, {''}, {'mRNA'}, 0, {''}, 599001, 624, true, {''}, meanHL, expression); + geneA28 = Gene(kb, NaN, {'GeneA28'}, {'Gene A28'}, {'genA28'}, {''}, {'mRNA'}, 0, {''}, 599725, 624, true, {''}, meanHL, expression); + geneA29 = Gene(kb, NaN, {'GeneA29'}, {'Gene A29'}, {'genA29'}, {''}, {'mRNA'}, 0, {''}, 600449, 624, true, {''}, meanHL, expression); + geneA30 = Gene(kb, NaN, {'GeneA30'}, {'Gene A30'}, {'genA30'}, {''}, {'mRNA'}, 0, {''}, 601173, 624, true, {''}, meanHL, expression); + geneA31 = Gene(kb, NaN, {'GeneA31'}, {'Gene A31'}, {'genA31'}, {''}, {'mRNA'}, 0, {''}, 601897, 624, true, {''}, meanHL, expression); + geneA32 = Gene(kb, NaN, {'GeneA32'}, {'Gene A32'}, {'genA32'}, {''}, {'mRNA'}, 0, {''}, 602621, 624, true, {''}, meanHL, expression); + geneA33 = Gene(kb, NaN, {'GeneA33'}, {'Gene A33'}, {'genA33'}, {''}, {'mRNA'}, 0, {''}, 603345, 624, true, {''}, meanHL, expression); + geneA34 = Gene(kb, NaN, {'GeneA34'}, {'Gene A34'}, {'genA34'}, {''}, {'mRNA'}, 0, {''}, 604069, 624, true, {''}, meanHL, expression); + geneA35 = Gene(kb, NaN, {'GeneA35'}, {'Gene A35'}, {'genA35'}, {''}, {'mRNA'}, 0, {''}, 604793, 624, true, {''}, meanHL, expression); + geneA36 = Gene(kb, NaN, {'GeneA36'}, {'Gene A36'}, {'genA36'}, {''}, {'mRNA'}, 0, {''}, 605517, 624, true, {''}, meanHL, expression); + geneA37 = Gene(kb, NaN, {'GeneA37'}, {'Gene A37'}, {'genA37'}, {''}, {'mRNA'}, 0, {''}, 606241, 624, true, {''}, meanHL, expression); + geneA38 = Gene(kb, NaN, {'GeneA38'}, {'Gene A38'}, {'genA38'}, {''}, {'mRNA'}, 0, {''}, 606965, 624, true, {''}, meanHL, expression); + geneA39 = Gene(kb, NaN, {'GeneA39'}, {'Gene A39'}, {'genA39'}, {''}, {'mRNA'}, 0, {''}, 607689, 624, true, {''}, meanHL, expression); + geneA40 = Gene(kb, NaN, {'GeneA40'}, {'Gene A40'}, {'genA40'}, {''}, {'mRNA'}, 0, {''}, 608413, 624, true, {''}, meanHL, expression); + geneA41 = Gene(kb, NaN, {'GeneA41'}, {'Gene A41'}, {'genA41'}, {''}, {'mRNA'}, 0, {''}, 609137, 624, true, {''}, meanHL, expression); + geneA42 = Gene(kb, NaN, {'GeneA42'}, {'Gene A42'}, {'genA42'}, {''}, {'mRNA'}, 0, {''}, 609861, 624, true, {''}, meanHL, expression); + geneA43 = Gene(kb, NaN, {'GeneA43'}, {'Gene A43'}, {'genA43'}, {''}, {'mRNA'}, 0, {''}, 610585, 624, true, {''}, meanHL, expression); + geneA44 = Gene(kb, NaN, {'GeneA44'}, {'Gene A44'}, {'genA44'}, {''}, {'mRNA'}, 0, {''}, 611309, 624, true, {''}, meanHL, expression); + geneA45 = Gene(kb, NaN, {'GeneA45'}, {'Gene A45'}, {'genA45'}, {''}, {'mRNA'}, 0, {''}, 612033, 624, true, {''}, meanHL, expression); + geneA46 = Gene(kb, NaN, {'GeneA46'}, {'Gene A46'}, {'genA46'}, {''}, {'mRNA'}, 0, {''}, 612757, 624, true, {''}, meanHL, expression); + geneA47 = Gene(kb, NaN, {'GeneA47'}, {'Gene A47'}, {'genA47'}, {''}, {'mRNA'}, 0, {''}, 613481, 624, true, {''}, meanHL, expression); + geneA48 = Gene(kb, NaN, {'GeneA48'}, {'Gene A48'}, {'genA48'}, {''}, {'mRNA'}, 0, {''}, 614205, 624, true, {''}, meanHL, expression); + geneA49 = Gene(kb, NaN, {'GeneA49'}, {'Gene A49'}, {'genA49'}, {''}, {'mRNA'}, 0, {''}, 614929, 624, true, {''}, meanHL, expression); + geneA50 = Gene(kb, NaN, {'GeneA50'}, {'Gene A50'}, {'genA50'}, {''}, {'mRNA'}, 0, {''}, 615653, 624, true, {''}, meanHL, expression); + tuA1 = TranscriptionUnit(kb, NaN, {'TuA1'}, {'Transcription unit A1'}, -35, 6, -35, 6, -1); + tuA2 = TranscriptionUnit(kb, NaN, {'TuA2'}, {'Transcription unit A2'}, -35, 6, -35, 6, -1); + tuA3 = TranscriptionUnit(kb, NaN, {'TuA3'}, {'Transcription unit A3'}, -35, 6, -35, 6, -1); + tuA4 = TranscriptionUnit(kb, NaN, {'TuA4'}, {'Transcription unit A4'}, -35, 6, -35, 6, -1); + tuA5 = TranscriptionUnit(kb, NaN, {'TuA5'}, {'Transcription unit A5'}, -35, 6, -35, 6, -1); + tuA6 = TranscriptionUnit(kb, NaN, {'TuA6'}, {'Transcription unit A6'}, -35, 6, -35, 6, -1); + tuA7 = TranscriptionUnit(kb, NaN, {'TuA7'}, {'Transcription unit A7'}, -35, 6, -35, 6, -1); + tuA8 = TranscriptionUnit(kb, NaN, {'TuA8'}, {'Transcription unit A8'}, -35, 6, -35, 6, -1); + tuA9 = TranscriptionUnit(kb, NaN, {'TuA9'}, {'Transcription unit A9'}, -35, 6, -35, 6, -1); + tuA10 = TranscriptionUnit(kb, NaN, {'TuA10'}, {'Transcription unit A10'}, -35, 6, -35, 6, -1); + tuA11 = TranscriptionUnit(kb, NaN, {'TuA11'}, {'Transcription unit A11'}, -35, 6, -35, 6, -1); + tuA12 = TranscriptionUnit(kb, NaN, {'TuA12'}, {'Transcription unit A12'}, -35, 6, -35, 6, -1); + tuA13 = TranscriptionUnit(kb, NaN, {'TuA13'}, {'Transcription unit A13'}, -35, 6, -35, 6, -1); + tuA14 = TranscriptionUnit(kb, NaN, {'TuA14'}, {'Transcription unit A14'}, -35, 6, -35, 6, -1); + tuA15 = TranscriptionUnit(kb, NaN, {'TuA15'}, {'Transcription unit A15'}, -35, 6, -35, 6, -1); + tuA16 = TranscriptionUnit(kb, NaN, {'TuA16'}, {'Transcription unit A16'}, -35, 6, -35, 6, -1); + tuA17 = TranscriptionUnit(kb, NaN, {'TuA17'}, {'Transcription unit A17'}, -35, 6, -35, 6, -1); + tuA18 = TranscriptionUnit(kb, NaN, {'TuA18'}, {'Transcription unit A18'}, -35, 6, -35, 6, -1); + tuA19 = TranscriptionUnit(kb, NaN, {'TuA19'}, {'Transcription unit A19'}, -35, 6, -35, 6, -1); + tuA20 = TranscriptionUnit(kb, NaN, {'TuA20'}, {'Transcription unit A20'}, -35, 6, -35, 6, -1); + tuA21 = TranscriptionUnit(kb, NaN, {'TuA21'}, {'Transcription unit A21'}, -35, 6, -35, 6, -1); + tuA22 = TranscriptionUnit(kb, NaN, {'TuA22'}, {'Transcription unit A22'}, -35, 6, -35, 6, -1); + tuA23 = TranscriptionUnit(kb, NaN, {'TuA23'}, {'Transcription unit A23'}, -35, 6, -35, 6, -1); + tuA24 = TranscriptionUnit(kb, NaN, {'TuA24'}, {'Transcription unit A24'}, -35, 6, -35, 6, -1); + tuA25 = TranscriptionUnit(kb, NaN, {'TuA25'}, {'Transcription unit A25'}, -35, 6, -35, 6, -1); + tuA26 = TranscriptionUnit(kb, NaN, {'TuA26'}, {'Transcription unit A26'}, -35, 6, -35, 6, -1); + tuA27 = TranscriptionUnit(kb, NaN, {'TuA27'}, {'Transcription unit A27'}, -35, 6, -35, 6, -1); + tuA28 = TranscriptionUnit(kb, NaN, {'TuA28'}, {'Transcription unit A28'}, -35, 6, -35, 6, -1); + tuA29 = TranscriptionUnit(kb, NaN, {'TuA29'}, {'Transcription unit A29'}, -35, 6, -35, 6, -1); + tuA30 = TranscriptionUnit(kb, NaN, {'TuA30'}, {'Transcription unit A30'}, -35, 6, -35, 6, -1); + tuA31 = TranscriptionUnit(kb, NaN, {'TuA31'}, {'Transcription unit A31'}, -35, 6, -35, 6, -1); + tuA32 = TranscriptionUnit(kb, NaN, {'TuA32'}, {'Transcription unit A32'}, -35, 6, -35, 6, -1); + tuA33 = TranscriptionUnit(kb, NaN, {'TuA33'}, {'Transcription unit A33'}, -35, 6, -35, 6, -1); + tuA34 = TranscriptionUnit(kb, NaN, {'TuA34'}, {'Transcription unit A34'}, -35, 6, -35, 6, -1); + tuA35 = TranscriptionUnit(kb, NaN, {'TuA35'}, {'Transcription unit A35'}, -35, 6, -35, 6, -1); + tuA36 = TranscriptionUnit(kb, NaN, {'TuA36'}, {'Transcription unit A36'}, -35, 6, -35, 6, -1); + tuA37 = TranscriptionUnit(kb, NaN, {'TuA37'}, {'Transcription unit A37'}, -35, 6, -35, 6, -1); + tuA38 = TranscriptionUnit(kb, NaN, {'TuA38'}, {'Transcription unit A38'}, -35, 6, -35, 6, -1); + tuA39 = TranscriptionUnit(kb, NaN, {'TuA39'}, {'Transcription unit A39'}, -35, 6, -35, 6, -1); + tuA40 = TranscriptionUnit(kb, NaN, {'TuA40'}, {'Transcription unit A40'}, -35, 6, -35, 6, -1); + tuA41 = TranscriptionUnit(kb, NaN, {'TuA41'}, {'Transcription unit A41'}, -35, 6, -35, 6, -1); + tuA42 = TranscriptionUnit(kb, NaN, {'TuA42'}, {'Transcription unit A42'}, -35, 6, -35, 6, -1); + tuA43 = TranscriptionUnit(kb, NaN, {'TuA43'}, {'Transcription unit A43'}, -35, 6, -35, 6, -1); + tuA44 = TranscriptionUnit(kb, NaN, {'TuA44'}, {'Transcription unit A44'}, -35, 6, -35, 6, -1); + tuA45 = TranscriptionUnit(kb, NaN, {'TuA45'}, {'Transcription unit A45'}, -35, 6, -35, 6, -1); + tuA46 = TranscriptionUnit(kb, NaN, {'TuA46'}, {'Transcription unit A46'}, -35, 6, -35, 6, -1); + tuA47 = TranscriptionUnit(kb, NaN, {'TuA47'}, {'Transcription unit A47'}, -35, 6, -35, 6, -1); + tuA48 = TranscriptionUnit(kb, NaN, {'TuA48'}, {'Transcription unit A48'}, -35, 6, -35, 6, -1); + tuA49 = TranscriptionUnit(kb, NaN, {'TuA49'}, {'Transcription unit A49'}, -35, 6, -35, 6, -1); + tuA50 = TranscriptionUnit(kb, NaN, {'TuA50'}, {'Transcription unit A50'}, -35, 6, -35, 6, -1); + monA1 = ProteinMonomer(kb, NaN, {'MonomerA1'}, {'Protein monomer A1'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA2 = ProteinMonomer(kb, NaN, {'MonomerA2'}, {'Protein monomer A2'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA3 = ProteinMonomer(kb, NaN, {'MonomerA3'}, {'Protein monomer A3'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA4 = ProteinMonomer(kb, NaN, {'MonomerA4'}, {'Protein monomer A4'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA5 = ProteinMonomer(kb, NaN, {'MonomerA5'}, {'Protein monomer A5'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA6 = ProteinMonomer(kb, NaN, {'MonomerA6'}, {'Protein monomer A6'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA7 = ProteinMonomer(kb, NaN, {'MonomerA7'}, {'Protein monomer A7'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA8 = ProteinMonomer(kb, NaN, {'MonomerA8'}, {'Protein monomer A8'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA9 = ProteinMonomer(kb, NaN, {'MonomerA9'}, {'Protein monomer A9'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA10 = ProteinMonomer(kb, NaN, {'MonomerA10'}, {'Protein monomer A10'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA11 = ProteinMonomer(kb, NaN, {'MonomerA11'}, {'Protein monomer A11'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA12 = ProteinMonomer(kb, NaN, {'MonomerA12'}, {'Protein monomer A12'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA13 = ProteinMonomer(kb, NaN, {'MonomerA13'}, {'Protein monomer A13'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA14 = ProteinMonomer(kb, NaN, {'MonomerA14'}, {'Protein monomer A14'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA15 = ProteinMonomer(kb, NaN, {'MonomerA15'}, {'Protein monomer A15'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA16 = ProteinMonomer(kb, NaN, {'MonomerA16'}, {'Protein monomer A16'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA17 = ProteinMonomer(kb, NaN, {'MonomerA17'}, {'Protein monomer A17'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA18 = ProteinMonomer(kb, NaN, {'MonomerA18'}, {'Protein monomer A18'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA19 = ProteinMonomer(kb, NaN, {'MonomerA19'}, {'Protein monomer A19'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA20 = ProteinMonomer(kb, NaN, {'MonomerA20'}, {'Protein monomer A20'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA21 = ProteinMonomer(kb, NaN, {'MonomerA21'}, {'Protein monomer A21'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA22 = ProteinMonomer(kb, NaN, {'MonomerA22'}, {'Protein monomer A22'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA23 = ProteinMonomer(kb, NaN, {'MonomerA23'}, {'Protein monomer A23'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA24 = ProteinMonomer(kb, NaN, {'MonomerA24'}, {'Protein monomer A24'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA25 = ProteinMonomer(kb, NaN, {'MonomerA25'}, {'Protein monomer A25'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA26 = ProteinMonomer(kb, NaN, {'MonomerA26'}, {'Protein monomer A26'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA27 = ProteinMonomer(kb, NaN, {'MonomerA27'}, {'Protein monomer A27'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA28 = ProteinMonomer(kb, NaN, {'MonomerA28'}, {'Protein monomer A28'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA29 = ProteinMonomer(kb, NaN, {'MonomerA29'}, {'Protein monomer A29'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA30 = ProteinMonomer(kb, NaN, {'MonomerA30'}, {'Protein monomer A30'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA31 = ProteinMonomer(kb, NaN, {'MonomerA31'}, {'Protein monomer A31'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA32 = ProteinMonomer(kb, NaN, {'MonomerA32'}, {'Protein monomer A32'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA33 = ProteinMonomer(kb, NaN, {'MonomerA33'}, {'Protein monomer A33'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA34 = ProteinMonomer(kb, NaN, {'MonomerA34'}, {'Protein monomer A34'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA35 = ProteinMonomer(kb, NaN, {'MonomerA35'}, {'Protein monomer A35'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA36 = ProteinMonomer(kb, NaN, {'MonomerA36'}, {'Protein monomer A36'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA37 = ProteinMonomer(kb, NaN, {'MonomerA37'}, {'Protein monomer A37'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA38 = ProteinMonomer(kb, NaN, {'MonomerA38'}, {'Protein monomer A38'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA39 = ProteinMonomer(kb, NaN, {'MonomerA39'}, {'Protein monomer A39'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA40 = ProteinMonomer(kb, NaN, {'MonomerA40'}, {'Protein monomer A40'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA41 = ProteinMonomer(kb, NaN, {'MonomerA41'}, {'Protein monomer A41'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA42 = ProteinMonomer(kb, NaN, {'MonomerA42'}, {'Protein monomer A42'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA43 = ProteinMonomer(kb, NaN, {'MonomerA43'}, {'Protein monomer A43'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA44 = ProteinMonomer(kb, NaN, {'MonomerA44'}, {'Protein monomer A44'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA45 = ProteinMonomer(kb, NaN, {'MonomerA45'}, {'Protein monomer A45'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA46 = ProteinMonomer(kb, NaN, {'MonomerA46'}, {'Protein monomer A46'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA47 = ProteinMonomer(kb, NaN, {'MonomerA47'}, {'Protein monomer A47'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA48 = ProteinMonomer(kb, NaN, {'MonomerA48'}, {'Protein monomer A48'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA49 = ProteinMonomer(kb, NaN, {'MonomerA49'}, {'Protein monomer A49'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + monA50 = ProteinMonomer(kb, NaN, {'MonomerA50'}, {'Protein monomer A50'}, {''}, {''}, {''}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, false, {''}, {''}, 0, {''}); + cpxAA1 = ProteinComplex(kb, NaN, {'ComplexAA1'}, {'Macromolecular complex AA1'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA2 = ProteinComplex(kb, NaN, {'ComplexAA2'}, {'Macromolecular complex AA2'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA3 = ProteinComplex(kb, NaN, {'ComplexAA3'}, {'Macromolecular complex AA3'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA4 = ProteinComplex(kb, NaN, {'ComplexAA4'}, {'Macromolecular complex AA4'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA5 = ProteinComplex(kb, NaN, {'ComplexAA5'}, {'Macromolecular complex AA5'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA6 = ProteinComplex(kb, NaN, {'ComplexAA6'}, {'Macromolecular complex AA6'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA7 = ProteinComplex(kb, NaN, {'ComplexAA7'}, {'Macromolecular complex AA7'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA8 = ProteinComplex(kb, NaN, {'ComplexAA8'}, {'Macromolecular complex AA8'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA9 = ProteinComplex(kb, NaN, {'ComplexAA9'}, {'Macromolecular complex AA9'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA10 = ProteinComplex(kb, NaN, {'ComplexAA10'}, {'Macromolecular complex AA10'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA11 = ProteinComplex(kb, NaN, {'ComplexAA11'}, {'Macromolecular complex AA11'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA12 = ProteinComplex(kb, NaN, {'ComplexAA12'}, {'Macromolecular complex AA12'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA13 = ProteinComplex(kb, NaN, {'ComplexAA13'}, {'Macromolecular complex AA13'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA14 = ProteinComplex(kb, NaN, {'ComplexAA14'}, {'Macromolecular complex AA14'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA15 = ProteinComplex(kb, NaN, {'ComplexAA15'}, {'Macromolecular complex AA15'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA16 = ProteinComplex(kb, NaN, {'ComplexAA16'}, {'Macromolecular complex AA16'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA17 = ProteinComplex(kb, NaN, {'ComplexAA17'}, {'Macromolecular complex AA17'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA18 = ProteinComplex(kb, NaN, {'ComplexAA18'}, {'Macromolecular complex AA18'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA19 = ProteinComplex(kb, NaN, {'ComplexAA19'}, {'Macromolecular complex AA19'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA20 = ProteinComplex(kb, NaN, {'ComplexAA20'}, {'Macromolecular complex AA20'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA21 = ProteinComplex(kb, NaN, {'ComplexAA21'}, {'Macromolecular complex AA21'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA22 = ProteinComplex(kb, NaN, {'ComplexAA22'}, {'Macromolecular complex AA22'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA23 = ProteinComplex(kb, NaN, {'ComplexAA23'}, {'Macromolecular complex AA23'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA24 = ProteinComplex(kb, NaN, {'ComplexAA24'}, {'Macromolecular complex AA24'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA25 = ProteinComplex(kb, NaN, {'ComplexAA25'}, {'Macromolecular complex AA25'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA26 = ProteinComplex(kb, NaN, {'ComplexAA26'}, {'Macromolecular complex AA26'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA27 = ProteinComplex(kb, NaN, {'ComplexAA27'}, {'Macromolecular complex AA27'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA28 = ProteinComplex(kb, NaN, {'ComplexAA28'}, {'Macromolecular complex AA28'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA29 = ProteinComplex(kb, NaN, {'ComplexAA29'}, {'Macromolecular complex AA29'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA30 = ProteinComplex(kb, NaN, {'ComplexAA30'}, {'Macromolecular complex AA30'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA31 = ProteinComplex(kb, NaN, {'ComplexAA31'}, {'Macromolecular complex AA31'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA32 = ProteinComplex(kb, NaN, {'ComplexAA32'}, {'Macromolecular complex AA32'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA33 = ProteinComplex(kb, NaN, {'ComplexAA33'}, {'Macromolecular complex AA33'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA34 = ProteinComplex(kb, NaN, {'ComplexAA34'}, {'Macromolecular complex AA34'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA35 = ProteinComplex(kb, NaN, {'ComplexAA35'}, {'Macromolecular complex AA35'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA36 = ProteinComplex(kb, NaN, {'ComplexAA36'}, {'Macromolecular complex AA36'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA37 = ProteinComplex(kb, NaN, {'ComplexAA37'}, {'Macromolecular complex AA37'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA38 = ProteinComplex(kb, NaN, {'ComplexAA38'}, {'Macromolecular complex AA38'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA39 = ProteinComplex(kb, NaN, {'ComplexAA39'}, {'Macromolecular complex AA39'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA40 = ProteinComplex(kb, NaN, {'ComplexAA40'}, {'Macromolecular complex AA40'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA41 = ProteinComplex(kb, NaN, {'ComplexAA41'}, {'Macromolecular complex AA41'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA42 = ProteinComplex(kb, NaN, {'ComplexAA42'}, {'Macromolecular complex AA42'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA43 = ProteinComplex(kb, NaN, {'ComplexAA43'}, {'Macromolecular complex AA43'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA44 = ProteinComplex(kb, NaN, {'ComplexAA44'}, {'Macromolecular complex AA44'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA45 = ProteinComplex(kb, NaN, {'ComplexAA45'}, {'Macromolecular complex AA45'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA46 = ProteinComplex(kb, NaN, {'ComplexAA46'}, {'Macromolecular complex AA46'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA47 = ProteinComplex(kb, NaN, {'ComplexAA47'}, {'Macromolecular complex AA47'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA48 = ProteinComplex(kb, NaN, {'ComplexAA48'}, {'Macromolecular complex AA48'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA49 = ProteinComplex(kb, NaN, {'ComplexAA49'}, {'Macromolecular complex AA49'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + cpxAA50 = ProteinComplex(kb, NaN, {'ComplexAA50'}, {'Macromolecular complex AA50'}, 10, {'dsDNA'}, {'dsDNA'}, {''}, {''}, {''}, {''}, {''}, {''}, {''}, {''}); + genome = kb.genome; + promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG'; + gene = 'ATGTCAAGATTAGATAAATCAAAAGTTATTAATTCAGCTTTAGAATTATTAAATGAAGTTGGTATTGAAGGTTTAACTACTAGAAAATTAGCTCAAAAATTAGGTGTTGAACAACCTACTTTATATTGGCATGTTAAAAATAAAAGAGCTTTATTAGATGCTTTAGCTATTGAAATGTTAGATAGACATCATACTCATTTTTGTCCTTTAGAAGGTGAATCATGGCAAGATTTTTTAAGAAATAATGCTAAATCATTTAGATGTGCTTTATTATCACATAGAGATGGTGCTAAAGTTCATTTAGGTACTAGACCTACTGAAAAACAATATGAAACTTTAGAAAATCAATTAGCTTTTTTATGTCAACAAGGTTTTTCATTAGAAAATGCTTTATATGCTTTATCAGCTGTTGGTCATTTTACTTTAGGTTGTGTTTTAGAAGATCAAGAACATCAAGTTGCTAAAGAAGAAAGAGAAACTCCTACTACTGATTCAATGCCTCCTTTATTAAGACAAGCTATTGAATTATTTGATCATCAAGGTGCTGAACCTGCTTTTTTATTTGGTTTAGAATTAATTATTTGTGGTTTAGAAAAACAATTAAAATGTGAATCAGGTTCATAA'; + genome.sequence = [genome.sequence repmat([promoter gene], [1, 50])]; + genome.sequenceLength = length(genome.sequence); + cytosol = kb.compartments(kb.cytosolCompartmentIndexs); + extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs); + geneA1.genome = genome; + geneA1.transcriptionUnits = tuA1; + geneA1.proteinMonomers = monA1; + geneA1.compartment = cytosol; + + geneA2.genome = genome; + geneA2.transcriptionUnits = tuA2; + geneA2.proteinMonomers = monA2; + geneA2.compartment = cytosol; + + geneA3.genome = genome; + geneA3.transcriptionUnits = tuA3; + geneA3.proteinMonomers = monA3; + geneA3.compartment = cytosol; + + geneA4.genome = genome; + geneA4.transcriptionUnits = tuA4; + geneA4.proteinMonomers = monA4; + geneA4.compartment = cytosol; + + geneA5.genome = genome; + geneA5.transcriptionUnits = tuA5; + geneA5.proteinMonomers = monA5; + geneA5.compartment = cytosol; + + geneA6.genome = genome; + geneA6.transcriptionUnits = tuA6; + geneA6.proteinMonomers = monA6; + geneA6.compartment = cytosol; + + geneA7.genome = genome; + geneA7.transcriptionUnits = tuA7; + geneA7.proteinMonomers = monA7; + geneA7.compartment = cytosol; + + geneA8.genome = genome; + geneA8.transcriptionUnits = tuA8; + geneA8.proteinMonomers = monA8; + geneA8.compartment = cytosol; + + geneA9.genome = genome; + geneA9.transcriptionUnits = tuA9; + geneA9.proteinMonomers = monA9; + geneA9.compartment = cytosol; + + geneA10.genome = genome; + geneA10.transcriptionUnits = tuA10; + geneA10.proteinMonomers = monA10; + geneA10.compartment = cytosol; + + geneA11.genome = genome; + geneA11.transcriptionUnits = tuA11; + geneA11.proteinMonomers = monA11; + geneA11.compartment = cytosol; + + geneA12.genome = genome; + geneA12.transcriptionUnits = tuA12; + geneA12.proteinMonomers = monA12; + geneA12.compartment = cytosol; + + geneA13.genome = genome; + geneA13.transcriptionUnits = tuA13; + geneA13.proteinMonomers = monA13; + geneA13.compartment = cytosol; + + geneA14.genome = genome; + geneA14.transcriptionUnits = tuA14; + geneA14.proteinMonomers = monA14; + geneA14.compartment = cytosol; + + geneA15.genome = genome; + geneA15.transcriptionUnits = tuA15; + geneA15.proteinMonomers = monA15; + geneA15.compartment = cytosol; + + geneA16.genome = genome; + geneA16.transcriptionUnits = tuA16; + geneA16.proteinMonomers = monA16; + geneA16.compartment = cytosol; + + geneA17.genome = genome; + geneA17.transcriptionUnits = tuA17; + geneA17.proteinMonomers = monA17; + geneA17.compartment = cytosol; + + geneA18.genome = genome; + geneA18.transcriptionUnits = tuA18; + geneA18.proteinMonomers = monA18; + geneA18.compartment = cytosol; + + geneA19.genome = genome; + geneA19.transcriptionUnits = tuA19; + geneA19.proteinMonomers = monA19; + geneA19.compartment = cytosol; + + geneA20.genome = genome; + geneA20.transcriptionUnits = tuA20; + geneA20.proteinMonomers = monA20; + geneA20.compartment = cytosol; + + geneA21.genome = genome; + geneA21.transcriptionUnits = tuA21; + geneA21.proteinMonomers = monA21; + geneA21.compartment = cytosol; + + geneA22.genome = genome; + geneA22.transcriptionUnits = tuA22; + geneA22.proteinMonomers = monA22; + geneA22.compartment = cytosol; + + geneA23.genome = genome; + geneA23.transcriptionUnits = tuA23; + geneA23.proteinMonomers = monA23; + geneA23.compartment = cytosol; + + geneA24.genome = genome; + geneA24.transcriptionUnits = tuA24; + geneA24.proteinMonomers = monA24; + geneA24.compartment = cytosol; + + geneA25.genome = genome; + geneA25.transcriptionUnits = tuA25; + geneA25.proteinMonomers = monA25; + geneA25.compartment = cytosol; + + geneA26.genome = genome; + geneA26.transcriptionUnits = tuA26; + geneA26.proteinMonomers = monA26; + geneA26.compartment = cytosol; + + geneA27.genome = genome; + geneA27.transcriptionUnits = tuA27; + geneA27.proteinMonomers = monA27; + geneA27.compartment = cytosol; + + geneA28.genome = genome; + geneA28.transcriptionUnits = tuA28; + geneA28.proteinMonomers = monA28; + geneA28.compartment = cytosol; + + geneA29.genome = genome; + geneA29.transcriptionUnits = tuA29; + geneA29.proteinMonomers = monA29; + geneA29.compartment = cytosol; + + geneA30.genome = genome; + geneA30.transcriptionUnits = tuA30; + geneA30.proteinMonomers = monA30; + geneA30.compartment = cytosol; + + geneA31.genome = genome; + geneA31.transcriptionUnits = tuA31; + geneA31.proteinMonomers = monA31; + geneA31.compartment = cytosol; + + geneA32.genome = genome; + geneA32.transcriptionUnits = tuA32; + geneA32.proteinMonomers = monA32; + geneA32.compartment = cytosol; + + geneA33.genome = genome; + geneA33.transcriptionUnits = tuA33; + geneA33.proteinMonomers = monA33; + geneA33.compartment = cytosol; + + geneA34.genome = genome; + geneA34.transcriptionUnits = tuA34; + geneA34.proteinMonomers = monA34; + geneA34.compartment = cytosol; + + geneA35.genome = genome; + geneA35.transcriptionUnits = tuA35; + geneA35.proteinMonomers = monA35; + geneA35.compartment = cytosol; + + geneA36.genome = genome; + geneA36.transcriptionUnits = tuA36; + geneA36.proteinMonomers = monA36; + geneA36.compartment = cytosol; + + geneA37.genome = genome; + geneA37.transcriptionUnits = tuA37; + geneA37.proteinMonomers = monA37; + geneA37.compartment = cytosol; + + geneA38.genome = genome; + geneA38.transcriptionUnits = tuA38; + geneA38.proteinMonomers = monA38; + geneA38.compartment = cytosol; + + geneA39.genome = genome; + geneA39.transcriptionUnits = tuA39; + geneA39.proteinMonomers = monA39; + geneA39.compartment = cytosol; + + geneA40.genome = genome; + geneA40.transcriptionUnits = tuA40; + geneA40.proteinMonomers = monA40; + geneA40.compartment = cytosol; + + geneA41.genome = genome; + geneA41.transcriptionUnits = tuA41; + geneA41.proteinMonomers = monA41; + geneA41.compartment = cytosol; + + geneA42.genome = genome; + geneA42.transcriptionUnits = tuA42; + geneA42.proteinMonomers = monA42; + geneA42.compartment = cytosol; + + geneA43.genome = genome; + geneA43.transcriptionUnits = tuA43; + geneA43.proteinMonomers = monA43; + geneA43.compartment = cytosol; + + geneA44.genome = genome; + geneA44.transcriptionUnits = tuA44; + geneA44.proteinMonomers = monA44; + geneA44.compartment = cytosol; + + geneA45.genome = genome; + geneA45.transcriptionUnits = tuA45; + geneA45.proteinMonomers = monA45; + geneA45.compartment = cytosol; + + geneA46.genome = genome; + geneA46.transcriptionUnits = tuA46; + geneA46.proteinMonomers = monA46; + geneA46.compartment = cytosol; + + geneA47.genome = genome; + geneA47.transcriptionUnits = tuA47; + geneA47.proteinMonomers = monA47; + geneA47.compartment = cytosol; + + geneA48.genome = genome; + geneA48.transcriptionUnits = tuA48; + geneA48.proteinMonomers = monA48; + geneA48.compartment = cytosol; + + geneA49.genome = genome; + geneA49.transcriptionUnits = tuA49; + geneA49.proteinMonomers = monA49; + geneA49.compartment = cytosol; + + geneA50.genome = genome; + geneA50.transcriptionUnits = tuA50; + geneA50.proteinMonomers = monA50; + geneA50.compartment = cytosol; + + tuA1.genome = genome; + tuA1.genes = geneA1; + tuA1.geneCompartments = cytosol; + tuA1.compartment = cytosol; + + tuA2.genome = genome; + tuA2.genes = geneA2; + tuA2.geneCompartments = cytosol; + tuA2.compartment = cytosol; + + tuA3.genome = genome; + tuA3.genes = geneA3; + tuA3.geneCompartments = cytosol; + tuA3.compartment = cytosol; + + tuA4.genome = genome; + tuA4.genes = geneA4; + tuA4.geneCompartments = cytosol; + tuA4.compartment = cytosol; + + tuA5.genome = genome; + tuA5.genes = geneA5; + tuA5.geneCompartments = cytosol; + tuA5.compartment = cytosol; + + tuA6.genome = genome; + tuA6.genes = geneA6; + tuA6.geneCompartments = cytosol; + tuA6.compartment = cytosol; + + tuA7.genome = genome; + tuA7.genes = geneA7; + tuA7.geneCompartments = cytosol; + tuA7.compartment = cytosol; + + tuA8.genome = genome; + tuA8.genes = geneA8; + tuA8.geneCompartments = cytosol; + tuA8.compartment = cytosol; + + tuA9.genome = genome; + tuA9.genes = geneA9; + tuA9.geneCompartments = cytosol; + tuA9.compartment = cytosol; + + tuA10.genome = genome; + tuA10.genes = geneA10; + tuA10.geneCompartments = cytosol; + tuA10.compartment = cytosol; + + tuA11.genome = genome; + tuA11.genes = geneA11; + tuA11.geneCompartments = cytosol; + tuA11.compartment = cytosol; + + tuA12.genome = genome; + tuA12.genes = geneA12; + tuA12.geneCompartments = cytosol; + tuA12.compartment = cytosol; + + tuA13.genome = genome; + tuA13.genes = geneA13; + tuA13.geneCompartments = cytosol; + tuA13.compartment = cytosol; + + tuA14.genome = genome; + tuA14.genes = geneA14; + tuA14.geneCompartments = cytosol; + tuA14.compartment = cytosol; + + tuA15.genome = genome; + tuA15.genes = geneA15; + tuA15.geneCompartments = cytosol; + tuA15.compartment = cytosol; + + tuA16.genome = genome; + tuA16.genes = geneA16; + tuA16.geneCompartments = cytosol; + tuA16.compartment = cytosol; + + tuA17.genome = genome; + tuA17.genes = geneA17; + tuA17.geneCompartments = cytosol; + tuA17.compartment = cytosol; + + tuA18.genome = genome; + tuA18.genes = geneA18; + tuA18.geneCompartments = cytosol; + tuA18.compartment = cytosol; + + tuA19.genome = genome; + tuA19.genes = geneA19; + tuA19.geneCompartments = cytosol; + tuA19.compartment = cytosol; + + tuA20.genome = genome; + tuA20.genes = geneA20; + tuA20.geneCompartments = cytosol; + tuA20.compartment = cytosol; + + tuA21.genome = genome; + tuA21.genes = geneA21; + tuA21.geneCompartments = cytosol; + tuA21.compartment = cytosol; + + tuA22.genome = genome; + tuA22.genes = geneA22; + tuA22.geneCompartments = cytosol; + tuA22.compartment = cytosol; + + tuA23.genome = genome; + tuA23.genes = geneA23; + tuA23.geneCompartments = cytosol; + tuA23.compartment = cytosol; + + tuA24.genome = genome; + tuA24.genes = geneA24; + tuA24.geneCompartments = cytosol; + tuA24.compartment = cytosol; + + tuA25.genome = genome; + tuA25.genes = geneA25; + tuA25.geneCompartments = cytosol; + tuA25.compartment = cytosol; + + tuA26.genome = genome; + tuA26.genes = geneA26; + tuA26.geneCompartments = cytosol; + tuA26.compartment = cytosol; + + tuA27.genome = genome; + tuA27.genes = geneA27; + tuA27.geneCompartments = cytosol; + tuA27.compartment = cytosol; + + tuA28.genome = genome; + tuA28.genes = geneA28; + tuA28.geneCompartments = cytosol; + tuA28.compartment = cytosol; + + tuA29.genome = genome; + tuA29.genes = geneA29; + tuA29.geneCompartments = cytosol; + tuA29.compartment = cytosol; + + tuA30.genome = genome; + tuA30.genes = geneA30; + tuA30.geneCompartments = cytosol; + tuA30.compartment = cytosol; + + tuA31.genome = genome; + tuA31.genes = geneA31; + tuA31.geneCompartments = cytosol; + tuA31.compartment = cytosol; + + tuA32.genome = genome; + tuA32.genes = geneA32; + tuA32.geneCompartments = cytosol; + tuA32.compartment = cytosol; + + tuA33.genome = genome; + tuA33.genes = geneA33; + tuA33.geneCompartments = cytosol; + tuA33.compartment = cytosol; + + tuA34.genome = genome; + tuA34.genes = geneA34; + tuA34.geneCompartments = cytosol; + tuA34.compartment = cytosol; + + tuA35.genome = genome; + tuA35.genes = geneA35; + tuA35.geneCompartments = cytosol; + tuA35.compartment = cytosol; + + tuA36.genome = genome; + tuA36.genes = geneA36; + tuA36.geneCompartments = cytosol; + tuA36.compartment = cytosol; + + tuA37.genome = genome; + tuA37.genes = geneA37; + tuA37.geneCompartments = cytosol; + tuA37.compartment = cytosol; + + tuA38.genome = genome; + tuA38.genes = geneA38; + tuA38.geneCompartments = cytosol; + tuA38.compartment = cytosol; + + tuA39.genome = genome; + tuA39.genes = geneA39; + tuA39.geneCompartments = cytosol; + tuA39.compartment = cytosol; + + tuA40.genome = genome; + tuA40.genes = geneA40; + tuA40.geneCompartments = cytosol; + tuA40.compartment = cytosol; + + tuA41.genome = genome; + tuA41.genes = geneA41; + tuA41.geneCompartments = cytosol; + tuA41.compartment = cytosol; + + tuA42.genome = genome; + tuA42.genes = geneA42; + tuA42.geneCompartments = cytosol; + tuA42.compartment = cytosol; + + tuA43.genome = genome; + tuA43.genes = geneA43; + tuA43.geneCompartments = cytosol; + tuA43.compartment = cytosol; + + tuA44.genome = genome; + tuA44.genes = geneA44; + tuA44.geneCompartments = cytosol; + tuA44.compartment = cytosol; + + tuA45.genome = genome; + tuA45.genes = geneA45; + tuA45.geneCompartments = cytosol; + tuA45.compartment = cytosol; + + tuA46.genome = genome; + tuA46.genes = geneA46; + tuA46.geneCompartments = cytosol; + tuA46.compartment = cytosol; + + tuA47.genome = genome; + tuA47.genes = geneA47; + tuA47.geneCompartments = cytosol; + tuA47.compartment = cytosol; + + tuA48.genome = genome; + tuA48.genes = geneA48; + tuA48.geneCompartments = cytosol; + tuA48.compartment = cytosol; + + tuA49.genome = genome; + tuA49.genes = geneA49; + tuA49.geneCompartments = cytosol; + tuA49.compartment = cytosol; + + tuA50.genome = genome; + tuA50.genes = geneA50; + tuA50.geneCompartments = cytosol; + tuA50.compartment = cytosol; + + monA1.gene = geneA1; + monA1.geneCompartments = cytosol; + monA1.compartment = cytosol; + + monA2.gene = geneA2; + monA2.geneCompartments = cytosol; + monA2.compartment = cytosol; + + monA3.gene = geneA3; + monA3.geneCompartments = cytosol; + monA3.compartment = cytosol; + + monA4.gene = geneA4; + monA4.geneCompartments = cytosol; + monA4.compartment = cytosol; + + monA5.gene = geneA5; + monA5.geneCompartments = cytosol; + monA5.compartment = cytosol; + + monA6.gene = geneA6; + monA6.geneCompartments = cytosol; + monA6.compartment = cytosol; + + monA7.gene = geneA7; + monA7.geneCompartments = cytosol; + monA7.compartment = cytosol; + + monA8.gene = geneA8; + monA8.geneCompartments = cytosol; + monA8.compartment = cytosol; + + monA9.gene = geneA9; + monA9.geneCompartments = cytosol; + monA9.compartment = cytosol; + + monA10.gene = geneA10; + monA10.geneCompartments = cytosol; + monA10.compartment = cytosol; + + monA11.gene = geneA11; + monA11.geneCompartments = cytosol; + monA11.compartment = cytosol; + + monA12.gene = geneA12; + monA12.geneCompartments = cytosol; + monA12.compartment = cytosol; + + monA13.gene = geneA13; + monA13.geneCompartments = cytosol; + monA13.compartment = cytosol; + + monA14.gene = geneA14; + monA14.geneCompartments = cytosol; + monA14.compartment = cytosol; + + monA15.gene = geneA15; + monA15.geneCompartments = cytosol; + monA15.compartment = cytosol; + + monA16.gene = geneA16; + monA16.geneCompartments = cytosol; + monA16.compartment = cytosol; + + monA17.gene = geneA17; + monA17.geneCompartments = cytosol; + monA17.compartment = cytosol; + + monA18.gene = geneA18; + monA18.geneCompartments = cytosol; + monA18.compartment = cytosol; + + monA19.gene = geneA19; + monA19.geneCompartments = cytosol; + monA19.compartment = cytosol; + + monA20.gene = geneA20; + monA20.geneCompartments = cytosol; + monA20.compartment = cytosol; + + monA21.gene = geneA21; + monA21.geneCompartments = cytosol; + monA21.compartment = cytosol; + + monA22.gene = geneA22; + monA22.geneCompartments = cytosol; + monA22.compartment = cytosol; + + monA23.gene = geneA23; + monA23.geneCompartments = cytosol; + monA23.compartment = cytosol; + + monA24.gene = geneA24; + monA24.geneCompartments = cytosol; + monA24.compartment = cytosol; + + monA25.gene = geneA25; + monA25.geneCompartments = cytosol; + monA25.compartment = cytosol; + + monA26.gene = geneA26; + monA26.geneCompartments = cytosol; + monA26.compartment = cytosol; + + monA27.gene = geneA27; + monA27.geneCompartments = cytosol; + monA27.compartment = cytosol; + + monA28.gene = geneA28; + monA28.geneCompartments = cytosol; + monA28.compartment = cytosol; + + monA29.gene = geneA29; + monA29.geneCompartments = cytosol; + monA29.compartment = cytosol; + + monA30.gene = geneA30; + monA30.geneCompartments = cytosol; + monA30.compartment = cytosol; + + monA31.gene = geneA31; + monA31.geneCompartments = cytosol; + monA31.compartment = cytosol; + + monA32.gene = geneA32; + monA32.geneCompartments = cytosol; + monA32.compartment = cytosol; + + monA33.gene = geneA33; + monA33.geneCompartments = cytosol; + monA33.compartment = cytosol; + + monA34.gene = geneA34; + monA34.geneCompartments = cytosol; + monA34.compartment = cytosol; + + monA35.gene = geneA35; + monA35.geneCompartments = cytosol; + monA35.compartment = cytosol; + + monA36.gene = geneA36; + monA36.geneCompartments = cytosol; + monA36.compartment = cytosol; + + monA37.gene = geneA37; + monA37.geneCompartments = cytosol; + monA37.compartment = cytosol; + + monA38.gene = geneA38; + monA38.geneCompartments = cytosol; + monA38.compartment = cytosol; + + monA39.gene = geneA39; + monA39.geneCompartments = cytosol; + monA39.compartment = cytosol; + + monA40.gene = geneA40; + monA40.geneCompartments = cytosol; + monA40.compartment = cytosol; + + monA41.gene = geneA41; + monA41.geneCompartments = cytosol; + monA41.compartment = cytosol; + + monA42.gene = geneA42; + monA42.geneCompartments = cytosol; + monA42.compartment = cytosol; + + monA43.gene = geneA43; + monA43.geneCompartments = cytosol; + monA43.compartment = cytosol; + + monA44.gene = geneA44; + monA44.geneCompartments = cytosol; + monA44.compartment = cytosol; + + monA45.gene = geneA45; + monA45.geneCompartments = cytosol; + monA45.compartment = cytosol; + + monA46.gene = geneA46; + monA46.geneCompartments = cytosol; + monA46.compartment = cytosol; + + monA47.gene = geneA47; + monA47.geneCompartments = cytosol; + monA47.compartment = cytosol; + + monA48.gene = geneA48; + monA48.geneCompartments = cytosol; + monA48.compartment = cytosol; + + monA49.gene = geneA49; + monA49.geneCompartments = cytosol; + monA49.compartment = cytosol; + + monA50.gene = geneA50; + monA50.geneCompartments = cytosol; + monA50.compartment = cytosol; + + cpxAA1.proteinMonomers = monA1; + cpxAA1.proteinMonomerCompartments = cytosol; + cpxAA1.proteinMonomerCoefficients = 4; + cpxAA1.compartment = cytosol; + cpxAA1.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA2.proteinMonomers = monA2; + cpxAA2.proteinMonomerCompartments = cytosol; + cpxAA2.proteinMonomerCoefficients = 4; + cpxAA2.compartment = cytosol; + cpxAA2.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA3.proteinMonomers = monA3; + cpxAA3.proteinMonomerCompartments = cytosol; + cpxAA3.proteinMonomerCoefficients = 4; + cpxAA3.compartment = cytosol; + cpxAA3.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA4.proteinMonomers = monA4; + cpxAA4.proteinMonomerCompartments = cytosol; + cpxAA4.proteinMonomerCoefficients = 4; + cpxAA4.compartment = cytosol; + cpxAA4.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA5.proteinMonomers = monA5; + cpxAA5.proteinMonomerCompartments = cytosol; + cpxAA5.proteinMonomerCoefficients = 4; + cpxAA5.compartment = cytosol; + cpxAA5.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA6.proteinMonomers = monA6; + cpxAA6.proteinMonomerCompartments = cytosol; + cpxAA6.proteinMonomerCoefficients = 4; + cpxAA6.compartment = cytosol; + cpxAA6.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA7.proteinMonomers = monA7; + cpxAA7.proteinMonomerCompartments = cytosol; + cpxAA7.proteinMonomerCoefficients = 4; + cpxAA7.compartment = cytosol; + cpxAA7.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA8.proteinMonomers = monA8; + cpxAA8.proteinMonomerCompartments = cytosol; + cpxAA8.proteinMonomerCoefficients = 4; + cpxAA8.compartment = cytosol; + cpxAA8.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA9.proteinMonomers = monA9; + cpxAA9.proteinMonomerCompartments = cytosol; + cpxAA9.proteinMonomerCoefficients = 4; + cpxAA9.compartment = cytosol; + cpxAA9.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA10.proteinMonomers = monA10; + cpxAA10.proteinMonomerCompartments = cytosol; + cpxAA10.proteinMonomerCoefficients = 4; + cpxAA10.compartment = cytosol; + cpxAA10.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA11.proteinMonomers = monA11; + cpxAA11.proteinMonomerCompartments = cytosol; + cpxAA11.proteinMonomerCoefficients = 4; + cpxAA11.compartment = cytosol; + cpxAA11.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA12.proteinMonomers = monA12; + cpxAA12.proteinMonomerCompartments = cytosol; + cpxAA12.proteinMonomerCoefficients = 4; + cpxAA12.compartment = cytosol; + cpxAA12.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA13.proteinMonomers = monA13; + cpxAA13.proteinMonomerCompartments = cytosol; + cpxAA13.proteinMonomerCoefficients = 4; + cpxAA13.compartment = cytosol; + cpxAA13.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA14.proteinMonomers = monA14; + cpxAA14.proteinMonomerCompartments = cytosol; + cpxAA14.proteinMonomerCoefficients = 4; + cpxAA14.compartment = cytosol; + cpxAA14.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA15.proteinMonomers = monA15; + cpxAA15.proteinMonomerCompartments = cytosol; + cpxAA15.proteinMonomerCoefficients = 4; + cpxAA15.compartment = cytosol; + cpxAA15.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA16.proteinMonomers = monA16; + cpxAA16.proteinMonomerCompartments = cytosol; + cpxAA16.proteinMonomerCoefficients = 4; + cpxAA16.compartment = cytosol; + cpxAA16.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA17.proteinMonomers = monA17; + cpxAA17.proteinMonomerCompartments = cytosol; + cpxAA17.proteinMonomerCoefficients = 4; + cpxAA17.compartment = cytosol; + cpxAA17.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA18.proteinMonomers = monA18; + cpxAA18.proteinMonomerCompartments = cytosol; + cpxAA18.proteinMonomerCoefficients = 4; + cpxAA18.compartment = cytosol; + cpxAA18.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA19.proteinMonomers = monA19; + cpxAA19.proteinMonomerCompartments = cytosol; + cpxAA19.proteinMonomerCoefficients = 4; + cpxAA19.compartment = cytosol; + cpxAA19.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA20.proteinMonomers = monA20; + cpxAA20.proteinMonomerCompartments = cytosol; + cpxAA20.proteinMonomerCoefficients = 4; + cpxAA20.compartment = cytosol; + cpxAA20.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA21.proteinMonomers = monA21; + cpxAA21.proteinMonomerCompartments = cytosol; + cpxAA21.proteinMonomerCoefficients = 4; + cpxAA21.compartment = cytosol; + cpxAA21.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA22.proteinMonomers = monA22; + cpxAA22.proteinMonomerCompartments = cytosol; + cpxAA22.proteinMonomerCoefficients = 4; + cpxAA22.compartment = cytosol; + cpxAA22.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA23.proteinMonomers = monA23; + cpxAA23.proteinMonomerCompartments = cytosol; + cpxAA23.proteinMonomerCoefficients = 4; + cpxAA23.compartment = cytosol; + cpxAA23.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA24.proteinMonomers = monA24; + cpxAA24.proteinMonomerCompartments = cytosol; + cpxAA24.proteinMonomerCoefficients = 4; + cpxAA24.compartment = cytosol; + cpxAA24.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA25.proteinMonomers = monA25; + cpxAA25.proteinMonomerCompartments = cytosol; + cpxAA25.proteinMonomerCoefficients = 4; + cpxAA25.compartment = cytosol; + cpxAA25.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA26.proteinMonomers = monA26; + cpxAA26.proteinMonomerCompartments = cytosol; + cpxAA26.proteinMonomerCoefficients = 4; + cpxAA26.compartment = cytosol; + cpxAA26.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA27.proteinMonomers = monA27; + cpxAA27.proteinMonomerCompartments = cytosol; + cpxAA27.proteinMonomerCoefficients = 4; + cpxAA27.compartment = cytosol; + cpxAA27.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA28.proteinMonomers = monA28; + cpxAA28.proteinMonomerCompartments = cytosol; + cpxAA28.proteinMonomerCoefficients = 4; + cpxAA28.compartment = cytosol; + cpxAA28.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA29.proteinMonomers = monA29; + cpxAA29.proteinMonomerCompartments = cytosol; + cpxAA29.proteinMonomerCoefficients = 4; + cpxAA29.compartment = cytosol; + cpxAA29.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA30.proteinMonomers = monA30; + cpxAA30.proteinMonomerCompartments = cytosol; + cpxAA30.proteinMonomerCoefficients = 4; + cpxAA30.compartment = cytosol; + cpxAA30.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA31.proteinMonomers = monA31; + cpxAA31.proteinMonomerCompartments = cytosol; + cpxAA31.proteinMonomerCoefficients = 4; + cpxAA31.compartment = cytosol; + cpxAA31.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA32.proteinMonomers = monA32; + cpxAA32.proteinMonomerCompartments = cytosol; + cpxAA32.proteinMonomerCoefficients = 4; + cpxAA32.compartment = cytosol; + cpxAA32.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA33.proteinMonomers = monA33; + cpxAA33.proteinMonomerCompartments = cytosol; + cpxAA33.proteinMonomerCoefficients = 4; + cpxAA33.compartment = cytosol; + cpxAA33.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA34.proteinMonomers = monA34; + cpxAA34.proteinMonomerCompartments = cytosol; + cpxAA34.proteinMonomerCoefficients = 4; + cpxAA34.compartment = cytosol; + cpxAA34.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA35.proteinMonomers = monA35; + cpxAA35.proteinMonomerCompartments = cytosol; + cpxAA35.proteinMonomerCoefficients = 4; + cpxAA35.compartment = cytosol; + cpxAA35.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA36.proteinMonomers = monA36; + cpxAA36.proteinMonomerCompartments = cytosol; + cpxAA36.proteinMonomerCoefficients = 4; + cpxAA36.compartment = cytosol; + cpxAA36.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA37.proteinMonomers = monA37; + cpxAA37.proteinMonomerCompartments = cytosol; + cpxAA37.proteinMonomerCoefficients = 4; + cpxAA37.compartment = cytosol; + cpxAA37.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA38.proteinMonomers = monA38; + cpxAA38.proteinMonomerCompartments = cytosol; + cpxAA38.proteinMonomerCoefficients = 4; + cpxAA38.compartment = cytosol; + cpxAA38.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA39.proteinMonomers = monA39; + cpxAA39.proteinMonomerCompartments = cytosol; + cpxAA39.proteinMonomerCoefficients = 4; + cpxAA39.compartment = cytosol; + cpxAA39.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA40.proteinMonomers = monA40; + cpxAA40.proteinMonomerCompartments = cytosol; + cpxAA40.proteinMonomerCoefficients = 4; + cpxAA40.compartment = cytosol; + cpxAA40.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA41.proteinMonomers = monA41; + cpxAA41.proteinMonomerCompartments = cytosol; + cpxAA41.proteinMonomerCoefficients = 4; + cpxAA41.compartment = cytosol; + cpxAA41.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA42.proteinMonomers = monA42; + cpxAA42.proteinMonomerCompartments = cytosol; + cpxAA42.proteinMonomerCoefficients = 4; + cpxAA42.compartment = cytosol; + cpxAA42.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA43.proteinMonomers = monA43; + cpxAA43.proteinMonomerCompartments = cytosol; + cpxAA43.proteinMonomerCoefficients = 4; + cpxAA43.compartment = cytosol; + cpxAA43.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA44.proteinMonomers = monA44; + cpxAA44.proteinMonomerCompartments = cytosol; + cpxAA44.proteinMonomerCoefficients = 4; + cpxAA44.compartment = cytosol; + cpxAA44.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA45.proteinMonomers = monA45; + cpxAA45.proteinMonomerCompartments = cytosol; + cpxAA45.proteinMonomerCoefficients = 4; + cpxAA45.compartment = cytosol; + cpxAA45.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA46.proteinMonomers = monA46; + cpxAA46.proteinMonomerCompartments = cytosol; + cpxAA46.proteinMonomerCoefficients = 4; + cpxAA46.compartment = cytosol; + cpxAA46.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA47.proteinMonomers = monA47; + cpxAA47.proteinMonomerCompartments = cytosol; + cpxAA47.proteinMonomerCoefficients = 4; + cpxAA47.compartment = cytosol; + cpxAA47.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA48.proteinMonomers = monA48; + cpxAA48.proteinMonomerCompartments = cytosol; + cpxAA48.proteinMonomerCoefficients = 4; + cpxAA48.compartment = cytosol; + cpxAA48.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA49.proteinMonomers = monA49; + cpxAA49.proteinMonomerCompartments = cytosol; + cpxAA49.proteinMonomerCoefficients = 4; + cpxAA49.compartment = cytosol; + cpxAA49.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + cpxAA50.proteinMonomers = monA50; + cpxAA50.proteinMonomerCompartments = cytosol; + cpxAA50.proteinMonomerCoefficients = 4; + cpxAA50.compartment = cytosol; + cpxAA50.complexFormationProcess = kb.processes.findobj('wholeCellModelID', 'Process_MacromolecularComplexation'); + + genome.genes = [genome.genes; geneA1; geneA2; geneA3; geneA4; geneA5; geneA6; geneA7; geneA8; geneA9; geneA10; geneA11; geneA12; geneA13; geneA14; geneA15; geneA16; geneA17; geneA18; geneA19; geneA20; geneA21; geneA22; geneA23; geneA24; geneA25; geneA26; geneA27; geneA28; geneA29; geneA30; geneA31; geneA32; geneA33; geneA34; geneA35; geneA36; geneA37; geneA38; geneA39; geneA40; geneA41; geneA42; geneA43; geneA44; geneA45; geneA46; geneA47; geneA48; geneA49; geneA50]; + genome.transcriptionUnits = [genome.transcriptionUnits; tuA1; tuA2; tuA3; tuA4; tuA5; tuA6; tuA7; tuA8; tuA9; tuA10; tuA11; tuA12; tuA13; tuA14; tuA15; tuA16; tuA17; tuA18; tuA19; tuA20; tuA21; tuA22; tuA23; tuA24; tuA25; tuA26; tuA27; tuA28; tuA29; tuA30; tuA31; tuA32; tuA33; tuA34; tuA35; tuA36; tuA37; tuA38; tuA39; tuA40; tuA41; tuA42; tuA43; tuA44; tuA45; tuA46; tuA47; tuA48; tuA49; tuA50]; + kb.genes = genome.genes; + kb.transcriptionUnits = genome.transcriptionUnits; + kb.proteinMonomers = [kb.proteinMonomers; monA1; monA2; monA3; monA4; monA5; monA6; monA7; monA8; monA9; monA10; monA11; monA12; monA13; monA14; monA15; monA16; monA17; monA18; monA19; monA20; monA21; monA22; monA23; monA24; monA25; monA26; monA27; monA28; monA29; monA30; monA31; monA32; monA33; monA34; monA35; monA36; monA37; monA38; monA39; monA40; monA41; monA42; monA43; monA44; monA45; monA46; monA47; monA48; monA49; monA50]; + kb.proteinComplexs = [kb.proteinComplexs; cpxAA1; cpxAA2; cpxAA3; cpxAA4; cpxAA5; cpxAA6; cpxAA7; cpxAA8; cpxAA9; cpxAA10; cpxAA11; cpxAA12; cpxAA13; cpxAA14; cpxAA15; cpxAA16; cpxAA17; cpxAA18; cpxAA19; cpxAA20; cpxAA21; cpxAA22; cpxAA23; cpxAA24; cpxAA25; cpxAA26; cpxAA27; cpxAA28; cpxAA29; cpxAA30; cpxAA31; cpxAA32; cpxAA33; cpxAA34; cpxAA35; cpxAA36; cpxAA37; cpxAA38; cpxAA39; cpxAA40; cpxAA41; cpxAA42; cpxAA43; cpxAA44; cpxAA45; cpxAA46; cpxAA47; cpxAA48; cpxAA49; cpxAA50]; + this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb); + + end function modifyNetworkParameters(~, sim) + g = sim.gene; + time = sim.state('Time'); + rna = sim.state('Rna'); + trn = sim.process('Transcription'); + nascentMRNAIndexs = find(any(rna.nascentRNAGeneComposition(g.mRNAIndexs, :), 1)); + [~, modTuIndexs] = ismember({'TuA1', 'TuA2', 'TuA3', 'TuA4', 'TuA5', 'TuA6', 'TuA7', 'TuA8', 'TuA9', 'TuA10', 'TuA11', 'TuA12', 'TuA13', 'TuA14', 'TuA15', 'TuA16', 'TuA17', 'TuA18', 'TuA19', 'TuA20', 'TuA21', 'TuA22', 'TuA23', 'TuA24', 'TuA25', 'TuA26', 'TuA27', 'TuA28', 'TuA29', 'TuA30', 'TuA31', 'TuA32', 'TuA33', 'TuA34', 'TuA35', 'TuA36', 'TuA37', 'TuA38', 'TuA39', 'TuA40', 'TuA41', 'TuA42', 'TuA43', 'TuA44', 'TuA45', 'TuA46', 'TuA47', 'TuA48', 'TuA49', 'TuA50'}, rna.wholeCellModelIDs(rna.nascentIndexs)); + tuBindProb = trn.transcriptionUnitBindingProbabilities; + meanBindProb = mean(tuBindProb(setdiff(nascentMRNAIndexs, modTuIndexs))); + rnaDecayRates = rna.decayRates(rna.matureIndexs); + modTuBindProb = tuBindProb; + modTuBindProb(modTuIndexs) = meanBindProb; + modTuBindProb(nascentMRNAIndexs) = modTuBindProb(nascentMRNAIndexs) * sum(tuBindProb(nascentMRNAIndexs)) / sum(modTuBindProb(nascentMRNAIndexs)); + modRnaExp = (rna.nascentRNAMatureRNAComposition * modTuBindProb) ./ (log(2) / time.cellCycleLength + rnaDecayRates); + modRnaExp = modRnaExp / sum(modRnaExp); + trn.transcriptionUnitBindingProbabilities = modTuBindProb; + rna.expression(rna.matureIndexs) = modRnaExp; + end + end +end \ No newline at end of file