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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 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 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