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