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

Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdóttir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu H.J. 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; Iñigo 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. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard 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, Sebastián N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdóttir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdóttir, Chiam Yu Ng, German Preciat, Alise Žagare, Siu H.J. Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto NoronhaAarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Iñigo 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. Aragón Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard Palsson, Ines Thiele, Ronan M.T. Fleming^*

^*Corresponding author for this work

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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
Pages (from-to)	639-702
Number of pages	64
Journal	Nature Protocols
Volume	14
Issue number	3
Early online date	20 Feb 2019
DOIs	https://doi.org/10.1038/s41596-018-0098-2
Publication status	Published - Mar 2019

Funding

The Reproducible Research Results (R3) team, in particular, C. Trefois and Y. Jarosz, of the Luxembourg Centre for Systems Biomedicine, is acknowledged for their help in setting up the virtual machine and the Jenkins server. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).

Funders	Funder number
Lilly Innovation
Minister of Economy and Competitiveness of Spain	BIO2016-77998-R
National Centre of Excellence in Research
U.S. Department of Energy
National Institute of General Medical Sciences	R35GM119850
Biological and Environmental Research	DE-SC0010429, 668738
Fonds National de la Recherche Luxembourg	FNR/O16/11402054, FNR/A12/01
Eusko Jaurlaritza	KK-2016/00026, PRE_2016_2_0044
Danmarks Tekniske Universitet
Novo Nordisk Fonden	AFR/6669348, NNF10CC1016517

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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0Final published version, 3.39 MBLicence: Article 25fa Dutch Copyright Act

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Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdóttir, H. S., Wachowiak, J., Keating, S. M., Vlasov, V., Magnusdóttir, S., Ng, C. Y., Preciat, G., Žagare, 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

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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.",

author = "Laurent Heirendt and Sylvain Arreckx and Thomas Pfau and Mendoza, {Sebasti{\'a}n N.} and Anne Richelle and Almut Heinken and Haraldsd{\'o}ttir, {Hulda S.} and Jacek Wachowiak and Keating, {Sarah M.} and Vanja Vlasov and Stefania Magnusd{\'o}ttir and Ng, {Chiam Yu} and German Preciat and Alise {\v Z}agare and Chan, {Siu H.J.} 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 I{\~n}igo 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 {Arag{\'o}n 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 Bernhard Palsson and Ines Thiele and Fleming, {Ronan M.T.}",

year = "2019",

month = mar,

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

language = "English",

volume = "14",

pages = "639--702",

journal = "Nature Protocols",

issn = "1754-2189",

publisher = "Nature Publishing Group",

number = "3",

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Heirendt, L, Arreckx, S, Pfau, T, Mendoza, SN, Richelle, A, Heinken, A, Haraldsdóttir, HS, Wachowiak, J, Keating, SM, Vlasov, V, Magnusdóttir, S, Ng, CY, Preciat, G, Žagare, 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, Aragón Artacho, FJ, Planes, FJ, Stalidzans, E, Maass, A, Vempala, S, Hucka, M, Saunders, MA, Maranas, CD, Lewis, NE, Sauter, T, Palsson, B, 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

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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, Sebastián N.

AU - Richelle, Anne

AU - Heinken, Almut

AU - Haraldsdóttir, Hulda S.

AU - Wachowiak, Jacek

AU - Keating, Sarah M.

AU - Vlasov, Vanja

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AU - Ng, Chiam Yu

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AU - Žagare, Alise

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AU - Aurich, Maike K.

AU - Clancy, Catherine M.

AU - Modamio, Jennifer

AU - Sauls, John T.

AU - Noronha, Alberto

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AU - Valcarcel, Luis V.

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AU - Ahookhosh, Masoud

AU - Ben Guebila, Marouen

AU - Kostromins, Andrejs

AU - Sompairac, Nicolas

AU - Le, Hoai M.

AU - Ma, Ding

AU - Sun, Yuekai

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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 - Aragón 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

AU - Thiele, Ines

AU - Fleming, Ronan M.T.

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

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