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Raw data and synthetic network source files from Purcell et al. 2013
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@bonnyjain
bonnyjain committed May 18, 2013
1 parent bb77f79 commit cea6522
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Binary file added data/GFPOptimizedTimeData.mat
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33 changes: 33 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene1.m
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classdef NoGene1 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
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
33 changes: 33 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene10.m
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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
33 changes: 33 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene100.m
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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
33 changes: 33 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene20.m
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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
33 changes: 33 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene5.m
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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
34 changes: 34 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene50.m
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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

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