Integrated Flux Balance Analysis Model of Escherichia coli

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1. Resource Description

   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. Keywords: central carbon metabolism, computational model, diauxic growth, Escherichia coli, flux-balance analysis, growth model, systems biology

2. Contact

   Karr, Jonathan, Ph.D.

3. Contact

   Covert, Markus

4. Contact

   Xiao, Nan

5. Contact

   Chen, Tiffany

6. Used by

   Stanford University

7. Operating System

   Any

8. Coded in

   MATLAB language