Skip to content

Commit cea6522

Browse files
bonnyjainbonnyjain
committed
Raw data and synthetic network source files from Purcell et al. 2013
1 parent bb77f79 commit cea6522

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

69 files changed

+39612
-0
lines changed

‎data/GFPOptimizedTimeData.mat

1.16 KB
Binary file not shown.

‎data/GFPRNAData.mat

1.5 KB
Binary file not shown.

‎data/GFPTimeData.mat

1.19 KB
Binary file not shown.

‎data/NoGeneRNAData.mat

1.51 KB
Binary file not shown.

‎data/NoGeneTimeData.mat

1.16 KB
Binary file not shown.

‎data/araCOptimizedTimeData.mat

1.15 KB
Binary file not shown.

‎data/araCRNAData.mat

1.48 KB
Binary file not shown.

‎data/araCTimeData.mat

1.18 KB
Binary file not shown.

‎data/lacIOptimizedTimeData.mat

1.18 KB
Binary file not shown.

‎data/lacIRNAData.mat

1.49 KB
Binary file not shown.

‎data/lacITimeData.mat

1.18 KB
Binary file not shown.

‎data/tetROptimizedTimeData.mat

1.19 KB
Binary file not shown.

‎data/tetRRNAData.mat

1.49 KB
Binary file not shown.

‎data/tetRTimeData.mat

1.18 KB
Binary file not shown.

‎src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene1.m

+33
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
classdef NoGene1 < edu.stanford.covert.cell.sim.runners.SimulationRunner
2+
methods
3+
function this = NoGene1(varargin)
4+
this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:});
5+
end
6+
end
7+
8+
methods (Access = protected)
9+
function modifyNetworkStructure(this, kb)
10+
import edu.stanford.covert.cell.kb.Gene;
11+
import edu.stanford.covert.cell.kb.ProteinMonomer;
12+
import edu.stanford.covert.cell.kb.ProteinComplex;
13+
import edu.stanford.covert.cell.kb.Stimuli;
14+
import edu.stanford.covert.cell.kb.TranscriptionUnit;
15+
meanHL = mean([kb.mRNAGenes.halfLife]);
16+
expression = zeros(1, 3);
17+
genome = kb.genome;
18+
promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG';
19+
lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA';
20+
genome.sequence = [genome.sequence repmat([promoter lacI], [1, 1])];
21+
genome.sequenceLength = length(genome.sequence);
22+
cytosol = kb.compartments(kb.cytosolCompartmentIndexs);
23+
extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs);
24+
this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb);
25+
end
26+
function modifyNetworkParameters(~, sim)
27+
g = sim.gene;
28+
time = sim.state('Time');
29+
rna = sim.state('Rna');
30+
trn = sim.process('Transcription');
31+
end
32+
end
33+
end

‎src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene10.m

+33
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
classdef NoGene10 < edu.stanford.covert.cell.sim.runners.SimulationRunner
2+
methods
3+
function this = NoGene10(varargin)
4+
this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:});
5+
end
6+
end
7+
8+
methods (Access = protected)
9+
function modifyNetworkStructure(this, kb)
10+
import edu.stanford.covert.cell.kb.Gene;
11+
import edu.stanford.covert.cell.kb.ProteinMonomer;
12+
import edu.stanford.covert.cell.kb.ProteinComplex;
13+
import edu.stanford.covert.cell.kb.Stimuli;
14+
import edu.stanford.covert.cell.kb.TranscriptionUnit;
15+
meanHL = mean([kb.mRNAGenes.halfLife]);
16+
expression = zeros(1, 3);
17+
genome = kb.genome;
18+
promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG';
19+
lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA';
20+
genome.sequence = [genome.sequence repmat([promoter lacI], [1, 10])];
21+
genome.sequenceLength = length(genome.sequence);
22+
cytosol = kb.compartments(kb.cytosolCompartmentIndexs);
23+
extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs);
24+
this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb);
25+
end
26+
function modifyNetworkParameters(~, sim)
27+
g = sim.gene;
28+
time = sim.state('Time');
29+
rna = sim.state('Rna');
30+
trn = sim.process('Transcription');
31+
end
32+
end
33+
end

‎src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene100.m

+33
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
classdef NoGene100 < edu.stanford.covert.cell.sim.runners.SimulationRunner
2+
methods
3+
function this = NoGene100(varargin)
4+
this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:});
5+
end
6+
end
7+
8+
methods (Access = protected)
9+
function modifyNetworkStructure(this, kb)
10+
import edu.stanford.covert.cell.kb.Gene;
11+
import edu.stanford.covert.cell.kb.ProteinMonomer;
12+
import edu.stanford.covert.cell.kb.ProteinComplex;
13+
import edu.stanford.covert.cell.kb.Stimuli;
14+
import edu.stanford.covert.cell.kb.TranscriptionUnit;
15+
meanHL = mean([kb.mRNAGenes.halfLife]);
16+
expression = zeros(1, 3);
17+
genome = kb.genome;
18+
promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG';
19+
lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA';
20+
genome.sequence = [genome.sequence repmat([promoter lacI], [1, 100])];
21+
genome.sequenceLength = length(genome.sequence);
22+
cytosol = kb.compartments(kb.cytosolCompartmentIndexs);
23+
extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs);
24+
this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb);
25+
end
26+
function modifyNetworkParameters(~, sim)
27+
g = sim.gene;
28+
time = sim.state('Time');
29+
rna = sim.state('Rna');
30+
trn = sim.process('Transcription');
31+
end
32+
end
33+
end

‎src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene20.m

+33
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
classdef NoGene20 < edu.stanford.covert.cell.sim.runners.SimulationRunner
2+
methods
3+
function this = NoGene20(varargin)
4+
this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:});
5+
end
6+
end
7+
8+
methods (Access = protected)
9+
function modifyNetworkStructure(this, kb)
10+
import edu.stanford.covert.cell.kb.Gene;
11+
import edu.stanford.covert.cell.kb.ProteinMonomer;
12+
import edu.stanford.covert.cell.kb.ProteinComplex;
13+
import edu.stanford.covert.cell.kb.Stimuli;
14+
import edu.stanford.covert.cell.kb.TranscriptionUnit;
15+
meanHL = mean([kb.mRNAGenes.halfLife]);
16+
expression = zeros(1, 3);
17+
genome = kb.genome;
18+
promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG';
19+
lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA';
20+
genome.sequence = [genome.sequence repmat([promoter lacI], [1, 20])];
21+
genome.sequenceLength = length(genome.sequence);
22+
cytosol = kb.compartments(kb.cytosolCompartmentIndexs);
23+
extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs);
24+
this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb);
25+
end
26+
function modifyNetworkParameters(~, sim)
27+
g = sim.gene;
28+
time = sim.state('Time');
29+
rna = sim.state('Rna');
30+
trn = sim.process('Transcription');
31+
end
32+
end
33+
end

‎src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene5.m

+33
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
classdef NoGene5 < edu.stanford.covert.cell.sim.runners.SimulationRunner
2+
methods
3+
function this = NoGene5(varargin)
4+
this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:});
5+
end
6+
end
7+
8+
methods (Access = protected)
9+
function modifyNetworkStructure(this, kb)
10+
import edu.stanford.covert.cell.kb.Gene;
11+
import edu.stanford.covert.cell.kb.ProteinMonomer;
12+
import edu.stanford.covert.cell.kb.ProteinComplex;
13+
import edu.stanford.covert.cell.kb.Stimuli;
14+
import edu.stanford.covert.cell.kb.TranscriptionUnit;
15+
meanHL = mean([kb.mRNAGenes.halfLife]);
16+
expression = zeros(1, 3);
17+
genome = kb.genome;
18+
promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG';
19+
lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA';
20+
genome.sequence = [genome.sequence repmat([promoter lacI], [1, 5])];
21+
genome.sequenceLength = length(genome.sequence);
22+
cytosol = kb.compartments(kb.cytosolCompartmentIndexs);
23+
extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs);
24+
this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb);
25+
end
26+
function modifyNetworkParameters(~, sim)
27+
g = sim.gene;
28+
time = sim.state('Time');
29+
rna = sim.state('Rna');
30+
trn = sim.process('Transcription');
31+
end
32+
end
33+
end

‎src/+edu/+stanford/+covert/+cell/+sim/+runners/NoGene50.m

+34
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
classdef NoGene50 < edu.stanford.covert.cell.sim.runners.SimulationRunner
2+
methods
3+
function this = NoGene50(varargin)
4+
this = this@edu.stanford.covert.cell.sim.runners.SimulationRunner(varargin{:});
5+
end
6+
end
7+
8+
methods (Access = protected)
9+
function modifyNetworkStructure(this, kb)
10+
import edu.stanford.covert.cell.kb.Gene;
11+
import edu.stanford.covert.cell.kb.ProteinMonomer;
12+
import edu.stanford.covert.cell.kb.ProteinComplex;
13+
import edu.stanford.covert.cell.kb.Stimuli;
14+
import edu.stanford.covert.cell.kb.TranscriptionUnit;
15+
meanHL = mean([kb.mRNAGenes.halfLife]);
16+
expression = zeros(1, 3);
17+
genome = kb.genome;
18+
promoter = 'TATCTACAGAGGCCCGCTTTAAGCATCCACGACCCTACTCACTTCAAAGTGGAACCACCCGTCGACGTGTGTCTTAACCCCTGCCGCTGCAAGGTGTGAG';
19+
lacI = 'ATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTAA';
20+
genome.sequence = [genome.sequence repmat([promoter lacI], [1, 50])];
21+
genome.sequenceLength = length(genome.sequence);
22+
cytosol = kb.compartments(kb.cytosolCompartmentIndexs);
23+
extracellularSpace = kb.compartments(kb.extracellularCompartmentIndexs);
24+
this.modifyNetworkStructure@edu.stanford.covert.cell.sim.runners.SimulationRunner(kb);
25+
26+
end
27+
function modifyNetworkParameters(~, sim)
28+
g = sim.gene;
29+
time = sim.state('Time');
30+
rna = sim.state('Rna');
31+
trn = sim.process('Transcription');
32+
end
33+
end
34+
end

0 commit comments

Comments
 (0)