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

@article{citeulike:1247054, 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.}, address = {Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, California 92093-0412, USA.}, author = {Becker, S. A. and Feist, A. M. and Mo, M. L. and Hannum, G. and Palsson, B. Ø. and Herrgard, M. J. }, citeulike-article-id = {1247054}, doi = {http://dx.doi.org/10.1038/nprot.2007.99}, issn = {1750-2799}, journal = {Nat Protoc}, keywords = {flux\_balance\_analysis, metabolism}, number = {3}, pages = {727--738}, posted-at = {2007-04-24 07:47:56}, priority = {4}, title = {Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.}, url = {http://dx.doi.org/10.1038/nprot.2007.99}, volume = {2}, year = {2007} }

TY - JOUR ID - citeulike:1247054 L3 - citeulike-article-id:1247054 TI - Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. JF - Nat Protoc VL - 2 IS - 3 SP - 727 EP - 738 AD - Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, California 92093-0412, USA. SN - 1750-2799 N2 - 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. KW - flux_balance_analysis KW - metabolism AU - Becker, SA AU - Feist, AM AU - Mo, ML AU - Hannum, G AU - Palsson, BØ AU - Herrgard, MJ PY - 2007/// UR - http://dx.doi.org/10.1038/nprot.2007.99 ER -