initial commit from 2605 of covertlab SVN repo

README.txt

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+This package provides the M. genitalium whole-cell knowledge base and simulation. 
+The script install.php installs the knowledge base and simulation, including 
+configuring the whole-cell model code for a Rocks Linux cluster. See install.php
+for installation instructions.
+
+
+Obtaining the knowledge, model, and simulation results
+=================================================================================
+All of the code, training data, and results of the whole-cell study are freely
+available at simtk.org/home/wholecell. All of the code, training data, and results
+are released under the MIT license. See license.txt for further information.
+
+
+About the M. genitalium Whole-Cell Model & Knowledge Base
+=================================================================================
+Please see the following manuscript and its accompanying supplementary information 
+for information about the construction of the whole-cell model.
+
+Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, 
+Glass JI, Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype. 
+In submission (2012).
+
+
+User Support
+=================================================================================
+Please contact the authors for help installing and/or using this
+software. See wholecell.stanford.edu for contact information.
+
+
+Development Team
+=================================================================================
+The M. genitalium whole cell model and knowledge base were developed at Stanford University by
+- Jonathan Karr, Graduate Student in Biophysics
+- Jayodita Sanghvi, Graduate Student in Bioengineering
+- Derek Macklin, Graduate Student in Bioengineering
+- Jared Jacobs, Software Engineer
+- Markus Covert, Assistant Professor of Bioengineering

build.sh

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+#!/bin/sh
+#
+# Compiles and runs tests. Arguments:
+#   1. target name (e.g. "runMediumTests" for runMediumTests.m)
+
+if [ ! -f "$1.m" ]
+then
+  echo No such file: $1.m
+  exit 1
+fi
+
+echo Compiling $1...
+
+rm -rf bin/$1
+mkdir -p bin/$1  
+./runMcc.pl runSimulation.prj $1
+chmod -R 775 bin/$1
+
+if [ $? -ne 0 ]
+then
+  echo Compile failed.
+  exit 1
+fi
+
+echo Compile succeeded
+exit 0

buildAndRunTests.sh

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+#!/bin/sh
+#
+# Compiles and runs tests. Arguments:
+#   1. target name (e.g. "runMediumTests" for runMediumTests.m)
+#   2. path to MATLAB Compiler Runtime (e.g. "/share/apps/MATLAB/MATLAB_Compiler_Runtime/v714")
+
+if [ ! -f "$1.m" ]
+then
+  echo No such file: $1.m
+  exit 1
+fi
+
+#build
+./build.sh $1
+if [[ $? -ne 0 ]]
+then
+  exit 1
+fi
+
+#run
+build=$1
+pathToRunTime=$2
+shift; shift;
+fname=$(mktemp $(dirname $(readlink -f $0))/tmp/test.out.XXXXXX)
+./run.sh $build $pathToRunTime $fname $*
+
+#parse output
+result="$(tail -2 $fname)"
+if [[ "$result" =~ "NO DISPLAY$" ]]
+then
+  result="$(tail -4 $fname)"
+  if [[ "$result" =~ "[Pp][Aa][Ss][Ss][Ee][Dd] in [0-9. a-z]*[.\s]*" ]]
+  then
+    exit 0
+  fi
+else
+  if [[ "$result" =~ "[Pp][Aa][Ss][Ss][Ee][Dd] in [0-9. a-z]*[.\s]*$" ]]
+  then
+    exit 0
+  fi
+fi
+exit 1

config.m

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+function dbConnectionParameters = config()
+%CONFIG Returns configuration values.
+%
+% Author: Jonathan Karr, jkarr@stanford.edu
+% Affilitation: Covert Lab, Department of Bioengineering, Stanford University
+% Last updated: 9/21/2010
+
+%% knowledgebase
+dbConnectionParameters.hostName = 'covertlab.stanford.edu';
+dbConnectionParameters.schema   = 'wholecell';
+dbConnectionParameters.userName = 'wholecell';
+dbConnectionParameters.password = 'wholecell';

data/allSimulationBatches.json

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+[
+	{id:'2012_01_03_20_29_11', timestamp:'2012_01_03_20_29_11', pbsid:'29470', date:'2012-01-03 20:29:11', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2261', nConditions:6, nSimulations:30},
+	{id:'2011_12_05_00_16_20', timestamp:'2011_12_05_00_16_20', pbsid:'23676', date:'2011-12-05 00:16:20', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2207', nConditions:16, nSimulations:80},
+	{id:'2011_11_11_21_29_19', timestamp:'2011_11_11_21_29_19', pbsid:'22313', date:'2011-11-11 21:29:19', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2176', nConditions:525, nSimulations:525},
+	{id:'2011_11_11_21_28_00', timestamp:'2011_11_11_21_28_00', pbsid:'21261', date:'2011-11-11 21:28:00', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2176', nConditions:525, nSimulations:525},
+	{id:'2011_11_11_21_25_46', timestamp:'2011_11_11_21_25_46', pbsid:'20209', date:'2011-11-11 21:25:46', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2176', nConditions:525, nSimulations:525},
+	{id:'2011_10_31_21_15_45', timestamp:'2011_10_31_21_15_45', pbsid:'19104', date:'2011-10-31 21:15:45', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2155', nConditions:525, nSimulations:525},
+	{id:'2011_10_26_19_26_15', timestamp:'2011_10_26_19_26_15', pbsid:'18052', date:'2011-10-26 19:26:15', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2149', nConditions:525, nSimulations:525},
+	{id:'2011_10_25_01_45_44', timestamp:'2011_10_25_01_45_44', pbsid:'17787', date:'2011-10-25 01:45:44', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2139', nConditions:1, nSimulations:128},
+	{id:'2011_10_20_10_09_12', timestamp:'2011_10_20_10_09_12', pbsid:'17117', date:'2011-10-20 10:09:12', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2129', nConditions:334, nSimulations:334},
+	{id:'2011_10_19_03_04_42', timestamp:'2011_10_19_03_04_42', pbsid:'16987', date:'2011-10-19 03:04:42', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2125', nConditions:64, nSimulations:64},
+	{id:'2011_10_19_02_53_45', timestamp:'2011_10_19_02_53_45', pbsid:'16850', date:'2011-10-19 02:53:45', firstName:'Jonathan', lastName:'Karr', affiliation:'Covert Lab, Department of Bioengineering, Stanford University', email:'jkarr@stanford.edu', userName:'jkarr', hostName:'covertlab-jkarr.Stanford.EDU', ipAddress:'171.65.92.146', revision:'2125', nConditions:1, nSimulations:64}
+]

data/fittedConstants.json

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+{"processes":{"ChromosomeCondensation":{},"ChromosomeSegregation":{},"Cytokinesis":{},"DNADamage":{},"DNARepair":{},"DNASupercoiling":{},"FtsZPolymerization":{},"HostInteraction":{},"MacromolecularComplexation":{},"Metabolism":{"macromoleculeStateInitializationGrowthFactor":[],"unaccountedEnergyConsumption":[]},"ProteinActivation":{},"ProteinDecay":{},"ProteinFolding":{},"ProteinModification":{},"ProteinProcessingI":{},"ProteinProcessingII":{},"ProteinTranslocation":{},"RNADecay":{},"RNAModification":{},"RNAProcessing":{},"Replication":{},"ReplicationInitiation":{},"RibosomeAssembly":{},"TerminalOrganelleAssembly":{},"Transcription":{"transcriptionUnitBindingProbabilities":[]},"TranscriptionalRegulation":{},"Translation":{},"tRNAAminoacylation":{}},"states":{"Chromosome":{},"FtsZRing":{},"Geometry":{},"Host":{},"Mass":{"dryWeightFractionCarbohydrate":[],"dryWeightFractionDNA":[],"dryWeightFractionIon":[],"dryWeightFractionLipid":[],"dryWeightFractionNucleotide":[],"dryWeightFractionPolyamine":[],"dryWeightFractionProtein":[],"dryWeightFractionRNA":[],"dryWeightFractionVitamin":[]},"MetabolicReaction":{},"Metabolite":{"biomassComposition":[],"biomassProduction":[],"byproducts":[]},"Polypeptide":{},"ProteinComplex":{},"ProteinMonomer":{},"RNAPolymerase":{},"Ribosome":{},"Rna":{"expression":[]},"Stimulus":{},"Time":{"replicationInitiationDuration":[]},"Transcript":{}}}