Reference : Creation and analysis of biochemical constraint-based models using the COBRA Toolbox ...
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
Systems Biomedicine
http://hdl.handle.net/10993/39264
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
English
Heirendt, Laurent mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Arreckx, Sylvain [> >]
Pfau, Thomas mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit]
Mendoza, Sebastian N. [> >]
Richelle, Anne [> >]
Heinken, Almut Katrin mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Haraldsdottir, Hulda S. [> >]
Wachowiak, Jacek [> >]
Keating, Sarah M. [> >]
Vlasov, Vanja mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Magnusdottir, Stefania [> >]
Ng, Chiam Yu [> >]
Preciat, German [> >]
Zagare, Alise mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Chan, Siu H. J. [> >]
Aurich, Maike K. [> >]
Clancy, Catherine M. [> >]
Modamio, Jennifer [> >]
Sauls, John T. [> >]
Noronha, Alberto mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Bordbar, Aarash [> >]
Cousins, Benjamin [> >]
El Assal, Diana Charles mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Valcarcel, Luis V. [> >]
Apaolaza, Inigo [> >]
Ghaderi, Susan mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Ahookhosh, Masoud [> >]
Ben Guebila, Marouen [> >]
Kostromins, Andrejs [> >]
Sompairac, Nicolas [> >]
Le, Hoai M. [> >]
Ma, Ding [> >]
Sun, Yuekai [> >]
Wang, Lin [> >]
Yurkovich, James T. [> >]
Oliveira, Miguel A. P. [> >]
Vuong, Phan T. [> >]
El Assal, Lemmer P. [> >]
Kuperstein, Inna [> >]
Zinovyev, Andrei [> >]
Hinton, H. Scott [> >]
Bryant, William A. [> >]
Aragon Artacho, Francisco J. [> >]
Planes, Francisco J. [> >]
Stalidzans, Egils [> >]
Maass, Alejandro [> >]
Vempala, Santosh [> >]
Hucka, Michael [> >]
Saunders, Michael A. [> >]
Maranas, Costas D. [> >]
Lewis, Nathan E. [> >]
Sauter, Thomas mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit]
Palsson, Bernhard O. [> >]
Thiele, Ines mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Fleming, Ronan M. T. [> >]
2019
Nature protocols
14
3
639-702
Yes
1750-2799
1750-2799
England
[en] 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.
http://hdl.handle.net/10993/39264
10.1038/s41596-018-0098-2

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