COBRApy swMATH ID: 16711 Software Authors: Ebrahim, Ali; Lerman, Joshua A; Palsson, Bernhard O; Hyduke, Daniel R Description: COBRApy: COnstraints-Based Reconstruction and Analysis for Python. Background: COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software. Results: Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes. Conclusion: COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. Availability: http://opencobra.sourceforge.net/ Homepage: http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-74 Related Software: COBRA Toolbox; Gurobi; CPLEX; DFBAlab; CVXPY; Matplotlib; RKHSMetaMod; SALib; sensitivity; meneco; fastGapFill; Clingo; Clingcon; MetaCyc; clasp; GloMIQO; MINOTAUR; FilMINT; SCIP; MIPLIB Cited in: 8 Documents all top 5 Cited by 29 Authors 2 Frioux, Clémence 1 Bockmayr, Alexander 1 Chew, Yin Hoon 1 Dochain, Denis 1 Gleixner, Ambros M. 1 Henk, Martin 1 Huet, Sylvie 1 Júlvez, Jorge 1 Klapper, Isaac 1 Labarthe, Simon 1 Malou, Thibault 1 Martinelli, Julien 1 Oliver, Stephen G. 1 Rapaport, Alain 1 Schaub, Torsten H. 1 Schellhorn, Sebastian 1 Sherman, David J. 1 Siegel, Anne 1 Spill, Fabian 1 Szyld, Daniel B. 1 Taupin, Marie-Luce 1 Taylor, Josh A. 1 Ugalde-Salas, Pablo 1 Wanko, Philipp 1 Wieder, Frederik 1 Yu, Xinli 1 Zengler, Karsten 1 Zhang, Tianyu 1 Zúñiga, Cristal Cited in 5 Serials 2 Bulletin of Mathematical Biology 1 Journal of Mathematical Biology 1 SIAM Journal on Applied Mathematics 1 Theory and Practice of Logic Programming 1 European Series in Applied and Industrial Mathematics (ESAIM): Proceedings and Surveys all top 5 Cited in 8 Fields 7 Biology and other natural sciences (92-XX) 3 Operations research, mathematical programming (90-XX) 1 Partial differential equations (35-XX) 1 Convex and discrete geometry (52-XX) 1 Statistics (62-XX) 1 Numerical analysis (65-XX) 1 Computer science (68-XX) 1 Systems theory; control (93-XX) Citations by Year