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NoGene50.m
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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