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Integrated Flux Balance Analysis Model of Escherichia coli
Publication Overview
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) Publication

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.

Available Downloads and Their Potential Uses: 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).

Purpose/Synopsis: 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.

Ontology Classification: Computational_Model, Physioloigcal_Model, Source_Code, Toolkit
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Keywords: central carbon metabolism, computational model, diauxic growth, Escherichia coli, flux-balance analysis, growth model, systems biology
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