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

Autor: Heirendt L; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Arreckx S; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Pfau T; Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg., Mendoza SN; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.; Mathomics, Center for Mathematical Modeling, University of Chile, Santiago, Chile., Richelle A; Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA., Heinken A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Haraldsdóttir HS; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Wachowiak J; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Keating SM; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK., Vlasov V; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Magnusdóttir S; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Ng CY; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA., Preciat G; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Žagare A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Chan SHJ; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA., Aurich MK; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Clancy CM; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Modamio J; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Sauls JT; Department of Physics, and Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA., Noronha A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Bordbar A; Sinopia Biosciences, San Diego, CA, USA., Cousins B; Algorithms and Randomness Center, School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA., El Assal DC; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Valcarcel LV; Biomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain., Apaolaza I; Biomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain., Ghaderi S; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Ahookhosh M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Ben Guebila M; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Kostromins A; Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia., Sompairac N; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France., Le HM; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Ma D; Department of Management Science and Engineering, Stanford University, Stanford, CA, USA., Sun Y; Department of Statistics, University of Michigan, Ann Arbor, MI, USA., Wang L; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA., Yurkovich JT; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA., Oliveira MAP; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Vuong PT; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., El Assal LP; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Kuperstein I; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France., Zinovyev A; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France., Hinton HS; Utah State University Research Foundation, North Logan, UT, USA., Bryant WA; Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK., Aragón Artacho FJ; Department of Mathematics, University of Alicante, Alicante, Spain., Planes FJ; Biomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain., Stalidzans E; Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia., Maass A; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.; Mathomics, Center for Mathematical Modeling, University of Chile, Santiago, Chile., Vempala S; Algorithms and Randomness Center, School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA., Hucka M; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA., Saunders MA; Department of Management Science and Engineering, Stanford University, Stanford, CA, USA., Maranas CD; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA., Lewis NE; Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA.; Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA., Sauter T; Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg., Palsson BØ; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark., Thiele I; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg., Fleming RMT; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg. ronan.mt.fleming@gmail.com.; Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, The Netherlands. ronan.mt.fleming@gmail.com.
Jazyk: angličtina
Zdroj: Nature protocols [Nat Protoc] 2019 Mar; Vol. 14 (3), pp. 639-702.
DOI: 10.1038/s41596-018-0098-2
Abstrakt: 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.
Databáze: MEDLINE