Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, Sebastian N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdottir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdottir, Chiam Yu Ng, German Preciat, Alise Zagare, Siu Hung Joshua Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto NoronhaAarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Inigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Miguel A. P. Oliveira, Phan T. Vuong, Lemmer P. El Assal, Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Francisco J. Aragon Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard O. Palsson, Ines Thiele, Ronan M. T. Fleming*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods.
Original languageEnglish
JournalNature Protocols
Volume14
Issue number3
Pages (from-to)639-702
Number of pages64
ISSN1750-2799
DOIs
Publication statusPublished - 2019

Cite this

Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., ... Fleming, R. M. T. (2019). Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols, 14(3), 639-702. https://doi.org/10.1038/s41596-018-0098-2