iFBA (Integrated Flux Balance Analysis Model of Escherichia coli) 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.
- Windows / MacOsX / Linux
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Covert, M.W., Xiao, N., Chen, T.J., and Karr, J.R. (2008)
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Bioinformatics. 24(18): 2044-2050.