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Markus W Covert, Nan Xiao, Tiffany J. Chen, and Jonathan R. Karr. Integrating Metabolic, Transcriptional Regulatory, and Signal Transduction Models in Escherichia Coli. Bioinformatics. 24(18):2044-2050 (2008)    View

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


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.

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Provides MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE.

Provides MATLAB, php, and latex code for all results and figures in Covert, Xiao, Chen, and Karr. Integrating Metabolic, Transcriptional Regulatory, and Signal Transduction Models in Escherichia Coli. Bioinformatics. 24(18):2044-2050 (2008).

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