Skip to content

Commit

Permalink
Raw data and synthetic network source files from Purcell et al. 2013
Browse files Browse the repository at this point in the history
  • Loading branch information
@bonnyjain
bonnyjain committed May 18, 2013
1 parent bb77f79 commit cea6522
Show file tree
Hide file tree
Showing 69 changed files with 39,612 additions and 0 deletions.
Binary file added data/GFPOptimizedTimeData.mat
View file
Binary file not shown.
Binary file added data/GFPRNAData.mat
View file
Binary file not shown.
Binary file added data/GFPTimeData.mat
View file
Binary file not shown.
Binary file added data/NoGeneRNAData.mat
View file
Binary file not shown.
Binary file added data/NoGeneTimeData.mat
View file
Binary file not shown.
Binary file added data/araCOptimizedTimeData.mat
View file
Binary file not shown.
Binary file added data/araCRNAData.mat
View file
Binary file not shown.
Binary file added data/araCTimeData.mat
View file
Binary file not shown.
Binary file added data/lacIOptimizedTimeData.mat
View file
Binary file not shown.
Binary file added data/lacIRNAData.mat
View file
Binary file not shown.
Binary file added data/lacITimeData.mat
View file
Binary file not shown.
Binary file added data/tetROptimizedTimeData.mat
View file
Binary file not shown.
Binary file added data/tetRRNAData.mat
View file
Binary file not shown.
Binary file added data/tetRTimeData.mat
View file
Binary file not shown.
33 changes: 33 additions & 0 deletions src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene1.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
classdef NoGene1 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
function this = NoGene1(varargin)
this = [email protected](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
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
classdef NoGene10 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
function this = NoGene10(varargin)
this = [email protected](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
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
classdef NoGene100 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
function this = NoGene100(varargin)
this = [email protected](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
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
classdef NoGene20 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
function this = NoGene20(varargin)
this = [email protected](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
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
classdef NoGene5 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
function this = NoGene5(varargin)
this = [email protected](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
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
classdef NoGene50 < edu.stanford.covert.cell.sim.runners.SimulationRunner
methods
function this = NoGene50(varargin)
this = [email protected](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
Loading

0 comments on commit cea6522

Please sign in to comment.