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