News

2014.01.09: modelBorgifier added to the Foundry

2013.10.01: E. coli ME-Model in Action

2013.08.17: GIM3E added to the Bakery

2013.08.17: Yeast M-Model 6.0  Published

2013.08.08: COBRA for Python App Note  Published

2013.04.19: COBRA for Python 0.2.1 Released

2013.03.13: Human Metabolism Recon 2.0  Published

2012.10.18: Paint4Net added to the Foundry

2012.08.07: The ME Generation in the Jacobs School News

2012.07.05: COBRA: The ME Generation Published

 

The COnstraints Based Reconstruction and Analysis (COBRA) approach to systems biology accepts the fact that we do not possess sufficiently detailed parameter data to precisely model, in the biophysical sense, an organism at the genome scale1.The COBRA approach focuses on employing physicochemical constraints to define the set of feasible states for a biological network in a given condition based on current knowledge. These constraints include compartmentalization, mass conservation, molecular crowding, and thermodynamic directionality.More recently, transcriptome data have been used to reduce the size of the set of computed feasible states. Although COBRA methods may not provide a unique solution, they provide a reduced set of solutions that may be used to guide biological hypothesis development. Given its initial success, COBRA has attracted attention from many investigators and has developed rapidly in recent years based on contributions from a growing number of laboratories – COBRA methods have been used in hundreds of studies.    


The openCOBRA project has arisen to provide researchers with easy access to core COBRA methodologies, and to provide a repository for community contributed modules that build off of these core COBRA Features.  The openCOBRA Project was initiated with tools for MATLAB but has now grown to include Python-based modules for dealing with the complex relationships of the next generation of COBRA models.


The openCOBRA project is currently maintained by Daniel R. Hyduke from Utah State University and Ali Ebrahim from UCSD.

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COBRA for MATLAB

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COBRA for Python aka cobra pie

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Links for Users

COBRA for Python

Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. 2013  COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Bio 7:74.


The COBRA Toolbox for MATLAB

Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. 2011 Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 6:1290-1307.

Citing COBRA for Python and the COBRA Toolbox