Please use the links below to use the free, hosted versions of our software and download source code.

In addition to the software packages listed here, we have also developed several utility libraries. These can be obtained from our MATLABCentral page.


The first "whole-cell" model of the bacterium M. genitalium. Provides all MATLAB simulation code, training data, detailed results, and MATLAB code for analysis of whole-cell simulations. Also provides an interactive web-based interface to the training data.


Web-based software for creating model organism databases for whole-cell models. Implemented in Python using the Django framework.


Database for storing and retrieving whole-cell simulations. Implemented in Python using the Django framework, h5py, and MySQL. Includes a web-based user interface developed using flot.


Web-based software for exploratory data analysis of whole-cell simulations. Implemented in JavaScript using jQuery, flot, and three.js.

Integrated flux-balance analysis (iFBA)

Provides MATLAB code and results for a computational model of E. coli which integrates an ordinary differential equation model of central carbon metabolism, a flux-balance analysis model of all of metabolism, and a Boolean model of transcriptional regulation.


Graphical user interface for easily creating signaling network diagrams animated with biomolecular data. Exports signaling diagrams to various formats including Flash. Provides all ActionScript and PHP code.


Whole-cell modeling summer school, April 2016

6-day summer school on whole-cell modeling featuring didactic lectures and hands-on tutorials with experts in computational and experimental systems biology.

  • Location: Center for Regulatory Genomics, Barcelona, Spain
  • Date: April 3-8 2016
  • Application deadline: November 2015
Whole-cell modeling workshop, March 2016

1-day workshop focused on developing standards for whole-cell modeling.

  • Location: Center for Interdisciplinary Research, Paris, France
  • Date: March 29, 2016
Whole-cell modeling/standards workshop, March 2015

5-day summer school focused on evaluating standards for whole-cell modeling.

  • Location: Rostock, Germany
  • Date: March 9-13, 2015
  • Application deadline: October 31, 2014


Graduate fellowships information

Collection of information about graduate fellowships and sample applications.