Software

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.

Whole-cell

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.

WholeCellKB

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

WholeCellSimDB

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.

WholeCellViz

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.

NetworkPainter

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.

Courses

Whole-cell modeling summer school, September 2017

4-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: September 4-7 2017
  • Application deadline: May 2017
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

Information

An introduction to whole-cell modeling

A primer on whole-cell modeling including the fundamentals of cell modeling, software engineering, scientific communication, and funding whole-cell modeling research. Includes detailed tutorials and coding exercises.

Whole-cell modeling forum

Forum for whole-cell modeling discussions.

Graduate fellowships information

Collection of information about graduate fellowships and sample applications.