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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas; Mendoza, Sebastián N; Richelle, Anne; Heinken, Almut; Haraldsdóttir, Hulda S; Wachowiak, Jacek; Keating, Sarah M; Vlasov, Vanja; Magnusdóttir, Stefania; Ng, Chiam Yu; Preciat, German; Zagare, Alise; Chan, Siu H J; Aurich, Maike K; Clancy, Catherine M; Modamio, Jennifer; Sauls, John T; Noronha, Alberto; Bordbar, Aarash; Cousins, Benjamin; El Assal, Diana C; Valcarcel, Luis V; Apaolaza, Iñigo; Ghaderi, Susan; 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; Aragón Artacho, Francisco J; Planes, Francisco J; Stalidzans, Egils; Maass, Alejandro; Vempala, Santosh; Hucka, Michael; Saunders, Michael A; Maranas, Costas D.
Afiliación
  • 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.
  • Richelle A; Mathomics, Center for Mathematical Modeling, University of Chile, Santiago, Chile.
  • Heinken A; Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA.
  • 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; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Vlasov V; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.
  • Magnusdóttir S; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Ng CY; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Preciat G; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
  • Zagare A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Chan SHJ; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Aurich MK; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
  • 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; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Noronha A; Department of Physics, and Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
  • Bordbar A; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Cousins B; Sinopia Biosciences, San Diego, CA, USA.
  • El Assal DC; Algorithms and Randomness Center, School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA.
  • Valcarcel LV; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Apaolaza I; Biomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain.
  • Ghaderi S; Biomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain.
  • 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; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Sompairac N; Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.
  • Le HM; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.
  • Ma D; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Sun Y; Department of Management Science and Engineering, Stanford University, Stanford, CA, USA.
  • Wang L; Department of Statistics, University of Michigan, Ann Arbor, MI, USA.
  • Yurkovich JT; Department of Chemical Engineering, The Pennsylvania State University, State College, PA, USA.
  • Oliveira MAP; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
  • 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; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
  • Zinovyev A; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.
  • Hinton HS; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.
  • Bryant WA; Utah State University Research Foundation, North Logan, UT, USA.
  • Aragón Artacho FJ; Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, UK.
  • Planes FJ; Department of Mathematics, University of Alicante, Alicante, Spain.
  • Stalidzans E; Biomedical Engineering and Sciences Department, TECNUN, University of Navarra, San Sebastián, Spain.
  • Maass A; Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.
  • Vempala S; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.
  • Hucka M; Mathomics, Center for Mathematical Modeling, University of Chile, Santiago, Chile.
  • Saunders MA; Algorithms and Randomness Center, School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA.
  • Maranas CD; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
Nat Protoc ; 14(3): 639-702, 2019 03.
Article en En | MEDLINE | ID: mdl-30787451
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.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Modelos Biológicos Tipo de estudio: Prognostic_studies Idioma: En Revista: Nat Protoc Año: 2019 Tipo del documento: Article País de afiliación: Luxemburgo
Texto completo
Imprimir
XML
PubMed Links
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Modelos Biológicos Tipo de estudio: Prognostic_studies Idioma: En Revista: Nat Protoc Año: 2019 Tipo del documento: Article País de afiliación: Luxemburgo