Mycoplasma genitalium whole-cell model
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lib
src/+edu/+stanford/+covert
src_test
.gitignore
README.txt
build.sh
buildAndRunTests.sh
compileSummary.pl
generateTestFixtures.m
getConfig.m
install.m
job.analysis.sh.tmpl
job.animation.sh.tmpl
job.dataexport.sh.tmpl
job.displacementCalculation.sh.tmpl
job.multiGenerationSimulation.sh.tmpl
job.reindexing.sh.tmpl
job.simulation.sh.tmpl
library.pl
license.txt
loadSimulation.m
mailSimulationsSummary.pl
run.sh
runAnalysis.m
runAnalysisTests.m
runAnimation.m
runAnimation.pl
runCellDivision.m
runChromosomeTests.m
runCoverageTests.m
runCoverageTests.sh
runDataExport.m
runDataExport.pl
runDisplacementCalculation.m
runDisplacementCalculation.pl
runLargeTests.m
runMcc.pl
runMediumDNATests.m
runMediumProteinTests.m
runMediumTests.m
runMultiGenerationSimulations.pl
runReindexing.m
runSimulation.m
runSimulation.prj
runSimulationTests.m
runSimulationTests.sh
runSimulations.pl
runSimulations.xsd
runSmallTests.m
setPath.m
setPreferences.m
setWarnings.m

README.txt

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