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 Noronha; Aarash 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

doi:10.1038/s41596-018-0098-2

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 Noronha

Aarash 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

University of Luxembourg
University of Chile
University of California at San Diego
European Bioinformatics Institute
Pennsylvania State University
Sinopia Biosciences
Georgia Institute of Technology
University of Navarra
University of Latvia
Institut national de la santé et de la recherche médicale
Stanford University
Michigan State University
University of Utah
Imperial College London
University of Alicante
California Institute of Technology

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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 language	English
Journal	Nature Protocols
Volume	14
Issue number	3
Pages (from-to)	639-702
Number of pages	64
ISSN	1754-2189
DOIs	https://doi.org/10.1038/s41596-018-0098-2
Publication status	Published - 2019

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Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdottir, H. S., Wachowiak, J., Keating, S. M., Vlasov, V., Magnusdottir, S., Ng, C. Y., Preciat, G., Zagare, A., Chan, S. H. J., Aurich, M. K., Clancy, C. M., Modamio, J., Sauls, J. T., ... 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

@article{abc863100a4040be9530faf60fc05c99,

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

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.",

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

year = "2019",

doi = "10.1038/s41596-018-0098-2",

language = "English",

volume = "14",

pages = "639--702",

journal = "Nature Protocols",

issn = "1754-2189",

publisher = "Springer Nature",

number = "3",

}

Heirendt, L, Arreckx, S, Pfau, T, Mendoza, SN, Richelle, A, Heinken, A, Haraldsdottir, HS, Wachowiak, J, Keating, SM, Vlasov, V, Magnusdottir, S, Ng, CY, Preciat, G, Zagare, A, Chan, SHJ, Aurich, MK, Clancy, CM, Modamio, J, Sauls, JT, Noronha, A, Bordbar, A, Cousins, B, El Assal, DC, Valcarcel, LV, Apaolaza, I, Ghaderi, S, Ahookhosh, M, Ben Guebila, M, Kostromins, A, Sompairac, N, Le, HM, Ma, D, Sun, Y, Wang, L, Yurkovich, JT, Oliveira, MAP, Vuong, PT, El Assal, LP, Kuperstein, I, Zinovyev, A, Hinton, HS, Bryant, WA, Aragon Artacho, FJ, Planes, FJ, Stalidzans, E, Maass, A, Vempala, S, Hucka, M, Saunders, MA, Maranas, CD, Lewis, NE, Sauter, T, Palsson, BO, Thiele, I & Fleming, RMT 2019, 'Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0', Nature Protocols, vol. 14, no. 3, pp. 639-702. https://doi.org/10.1038/s41596-018-0098-2

TY - JOUR

T1 - Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

AU - Heirendt, Laurent

AU - Arreckx, Sylvain

AU - Pfau, Thomas

AU - Mendoza, Sebastian N.

AU - Richelle, Anne

AU - Heinken, Almut

AU - Haraldsdottir, Hulda S.

AU - Wachowiak, Jacek

AU - Keating, Sarah M.

AU - Vlasov, Vanja

AU - Magnusdottir, Stefania

AU - Ng, Chiam Yu

AU - Preciat, German

AU - Zagare, Alise

AU - Chan, Siu Hung Joshua

AU - Aurich, Maike K.

AU - Clancy, Catherine M.

AU - Modamio, Jennifer

AU - Sauls, John T.

AU - Noronha, Alberto

AU - Bordbar, Aarash

AU - Cousins, Benjamin

AU - El Assal, Diana C.

AU - Valcarcel, Luis V.

AU - Apaolaza, Inigo

AU - Ghaderi, Susan

AU - Ahookhosh, Masoud

AU - Ben Guebila, Marouen

AU - Kostromins, Andrejs

AU - Sompairac, Nicolas

AU - Le, Hoai M.

AU - Ma, Ding

AU - Sun, Yuekai

AU - Wang, Lin

AU - Yurkovich, James T.

AU - Oliveira, Miguel A. P.

AU - Vuong, Phan T.

AU - El Assal, Lemmer P.

AU - Kuperstein, Inna

AU - Zinovyev, Andrei

AU - Hinton, H. Scott

AU - Bryant, William A.

AU - Aragon Artacho, Francisco J.

AU - Planes, Francisco J.

AU - Stalidzans, Egils

AU - Maass, Alejandro

AU - Vempala, Santosh

AU - Hucka, Michael

AU - Saunders, Michael A.

AU - Maranas, Costas D.

AU - Lewis, Nathan E.

AU - Sauter, Thomas

AU - Palsson, Bernhard O.

AU - Thiele, Ines

AU - Fleming, Ronan M. T.

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

U2 - 10.1038/s41596-018-0098-2

DO - 10.1038/s41596-018-0098-2

M3 - Journal article

C2 - 30787451

SN - 1754-2189

VL - 14

SP - 639

EP - 702

JO - Nature Protocols

JF - Nature Protocols

IS - 3

ER -

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

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