Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.

TitleQuantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
Publication TypeJournal Article
Year of Publication2007
AuthorsBecker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ
JournalNature protocols
Volume2
Issue3
Pagination727-38
PubMed Date2007
ISSN1750-2799
KeywordsCells, Computational Biology, Computer Simulation, Metabolic Networks and Pathways, Models, Biological, Software, Systems Biology
Abstract

The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-based reconstruction and analysis toolbox, a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraint-based approach. Specifically, this software allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules. Functions enabling these calculations are included in the toolbox, allowing a user to input a genome-scale metabolic model distributed in Systems Biology Markup Language format and perform these calculations with just a few lines of code. The results are predictions of cellular behavior that have been verified as accurate in a growing body of research. After software installation, calculation time is minimal, allowing the user to focus on the interpretation of the computational results.

Alternate JournalNat Protoc
PubMed ID17406635

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