Integrated Flux Balance Analysis Model of Escherichia coli

Overview

This project includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) -- a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations.

Purpose

Provides MATLAB scripts for simulating metabolism by an integrated flux balance analysis / boolean regulatory / ODE kinetic approach.

Audience

Biologists interested in bacterial metabolism. Computational biologists interested in integration of multiple modeling approaches including flux balance analysis, boolean regulatory logic, and detailed ODE kinetic models, for the purpose of large-scale cellular modeling.

Long Term Goals and Related Uses

Build increasing comprehensive models of cellular physiology by integrating models of various cellular processes, each of which may be best described using different representation.

Documents

• Animations [html]
• Manuscript [pdf | html]
• Supplement [pdf]
• Posters [BCATS, CSB (pdf) | BMI (pdf)]
• MATLAB scripts [zip]
• Complete Archive (MATLAB scripts, latex files, cache version of simulations, documentation) [zip]
• Documentation [html]
• SimTK Project Site [html]

References

Covert, M.W., Xiao, N., Chen, T.J., and Karr, J.R. (2008) Integrated Flux Balance Analysis Model of Escherichia coli. Bioinformatics. 24(18): 2044-2050.