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

被引：740

作者：

Heirendt, Laurent ^{[1
,2
]}

Arreckx, Sylvain ^{[1
]}

Pfau, Thomas ^{[2
]}

Mendoza, Sebastian N. ^{[3
,4
]}

Richelle, Anne ^{[5
]}

Heinken, Almut ^{[1
]}

Haraldsdottir, Hulda S. ^{[1
]}

Wachowiak, Jacek ^{[1
]}

Keating, Sarah M. ^{[6
]}

Vlasov, Vanja ^{[1
]}

Magnusdottir, Stefania ^{[1
]}

Ng, Chiam Yu ^{[7
]}

Preciat, German ^{[1
]}

Zagare, Alise ^{[1
]}

Chan, Siu H. J. ^{[7
]}

Aurich, Maike K. ^{[1
]}

Clancy, Catherine M. ^{[1
]}

Modamio, Jennifer ^{[1
]}

Sauls, John T. ^{[8
,9
]}

Noronha, Alberto ^{[1
]}

Bordbar, Aarash ^{[10
]}

Cousins, Benjamin ^{[11
]}

El Assal, Diana C. ^{[1
]}

Valcarcel, Luis V. ^{[12
]}

Apaolaza, Inigo ^{[12
]}

Ghaderi, Susan ^{[1
]}

Ahookhosh, Masoud ^{[1
]}

Ben Guebila, Marouen ^{[1
]}

Kostromins, Andrejs ^{[13
]}

Sompairac, Nicolas ^{[14
]}

Le, Hoai M. ^{[1
]}

Ma, Ding ^{[15
]}

Sun, Yuekai ^{[16
]}

Wang, Lin ^{[7
]}

Yurkovich, James T. ^{[17
]}

Oliveira, Miguel A. P. ^{[1
]}

Vuong, Phan T. ^{[1
]}

El Assal, Lemmer P. ^{[1
]}

Kuperstein, Inna ^{[14
]}

Zinovyev, Andrei ^{[14
]}

Hinton, H. Scott ^{[18
]}

Bryant, William A. ^{[19
]}

Aragon Artacho, Francisco J. ^{[20
]}

Planes, Francisco J. ^{[12
]}

Stalidzans, Egils ^{[13
]}

Maass, Alejandro ^{[3
,4
]}

Vempala, Santosh ^{[11
]}

Hucka, Michael ^{[21
]}

Saunders, Michael A. ^{[15
]}

Maranas, Costas D. ^{[7
]}

机构：

[1] Univ Luxembourg, Luxembourg Ctr Syst Biomed, Belvaux, Luxembourg

[2] Univ Luxembourg, Life Sci Res Unit, Belvaux, Luxembourg

[3] Univ Chile, Ctr Genome Regulat Fondap 15090007, Santiago, Chile

[4] Univ Chile, Ctr Math Modeling, Math, Santiago, Chile

[5] Univ Calif San Diego, Sch Med, Dept Pediat, La Jolla, CA 92093 USA

[6] EBI, EMBL, Cambridge, England

[7] Penn State Univ, Dept Chem Engn, State Coll, PA USA

[8] Univ Calif San Diego, Dept Phys, La Jolla, CA USA

[9] Univ Calif San Diego, Bioinformat & Syst Biol Program, La Jolla, CA USA

[10] Sinopia Biosci, San Diego, CA USA

[11] Georgia Inst Technol, Sch Comp Sci, Algorithms & Randomness Ctr, Atlanta, GA 30332 USA

[12] Univ Navarra, Biomed Engn & Sci Dept, TECNUN, San Sebastian, Spain

[13] Univ Latvia, Inst Microbiol & Biotechnol, Riga, Latvia

[14] INSERM, U900, PSL Res Univ, Inst Curie,Mines Paris Tech, F-U900 Paris, France

[15] Stanford Univ, Dept Management Sci & Engn, Stanford, CA 94305 USA

[16] Univ Michigan, Dept Stat, Ann Arbor, MI 48109 USA

[17] Univ Calif San Diego, Dept Bioengn, La Jolla, CA USA

[18] Utah State Univ, Res Fdn, North Logan, UT USA

[19] Imperial Coll London, Dept Life Sci, Ctr Integrat Syst Biol & Bioinformat, London, England

[20] Univ Alicante, Dept Math, Alicante, Spain

[21] CALTECH, Dept Comp & Math Sci, Pasadena, CA 91125 USA

[22] Univ Calif San Diego, Novo Nordisk Fdn Ctr Biosustainabil, La Jolla, CA USA

[23] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, Lyngby, Denmark

[24] Leiden Univ, Fac Sci, Leiden Acad Ctr Drug Res, Div Syst Biomed & Pharmacol, Leiden, Netherlands

来源：

NATURE PROTOCOLS | 2019年 / 14卷 / 03期

关键词：

GENOME-SCALE MODELS; SYSTEMS BIOLOGY; METABOLIC NETWORK; QUANTITATIVE PREDICTION; GLOBAL RECONSTRUCTION; CELLULAR-METABOLISM; PARKINSONS-DISEASE; INBORN-ERRORS; BALANCE; STRAIN;

D O I：

10.1038/s41596-018-0098-2

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：639 / 702

页数：64

共 155 条

[51] FBA-SimVis: interactive visualization of constraint-based metabolic models [J].

Grafahrend-Belau, Eva ;

Klukas, Christian ;

Junker, Bjoern H. ;

Schreiber, Falk .

BIOINFORMATICS, 2009, 25 (20) :2755-2757

[52] Computationally efficient flux variability analysis [J].

Gudmundsson, Steinn ;

Thiele, Ines .

BMC BIOINFORMATICS, 2010, 11

[53] Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction [J].

Haraldsdottir, H. S. ;

Thiele, I. ;

Fleming, R. M. T. .

BIOPHYSICAL JOURNAL, 2012, 102 (08) :1703-1711

[54] CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models [J].

Haraldsdottir, Hulda S. ;

Cousins, Ben ;

Thiele, Ines ;

Fleming, Ronan M. T. ;

Vempala, Santosh .

BIOINFORMATICS, 2017, 33 (11) :1741-1743

[55] Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks [J].

Haraldsdottir, Hulda S. ;

Fleming, Ronan M. T. .

PLOS COMPUTATIONAL BIOLOGY, 2016, 12 (11)

[56] Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2 [J].

Haraldsdottir, Hulda S. ;

Thiele, Ines ;

Fleming, Ronan M. T. .

JOURNAL OF CHEMINFORMATICS, 2014, 6

[57] The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 [J].

Hastings, Janna ;

de Matos, Paula ;

Dekker, Adriano ;

Ennis, Marcus ;

Harsha, Bhavana ;

Kale, Namrata ;

Muthukrishnan, Venkatesh ;

Owen, Gareth ;

Turner, Steve ;

Williams, Mark ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D456-D463

[58] A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism [J].

Hefzi, Hooman ;

Ang, Kok Siong ;

Hanscho, Michael ;

Bordbar, Aarash ;

Ruckerbauer, David ;

Lakshmanan, Meiyappan ;

Orellana, Camila A. ;

Baycin-Hizal, Deniz ;

Huang, Yingxiang ;

Ley, Daniel ;

Martinez, Veronica S. ;

Kyriakopoulos, Sarantos ;

Jimenez, Natalia E. ;

Zielinski, Daniel C. ;

Quek, Lake-Ee ;

Wulff, Tune ;

Arnsdorf, Johnny ;

Li, Shangzhong ;

Lee, Jae Seong ;

Paglia, Giuseppe ;

Loira, Nicolas ;

Spahn, Philipp N. ;

Pedersen, Lasse E. ;

Gutierrez, Jahir M. ;

King, Zachary A. ;

Lund, Anne Mathilde ;

Nagarajan, Harish ;

Thomas, Alex ;

Abdel-Haleem, Alyaa M. ;

Zanghellini, Juergen ;

Kildegaard, Helene F. ;

Voldborg, Bjorn G. ;

Gerdtzen, Ziomara P. ;

Betenbaugh, Michael J. ;

Palsson, Bernhard O. ;

Andersen, Mikael R. ;

Nielsen, Lars K. ;

Borth, Nicole ;

Lee, Dong-Yup ;

Lewis, Nathan E. .

CELL SYSTEMS, 2016, 3 (05) :434-+

[59] Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe [J].

Heinken, Almut ;

Khan, M. Tanweer ;

Paglia, Giuseppe ;

Rodionov, Dmitry A. ;

Harmsen, Hermie J. M. ;

Thiele, Ines .

JOURNAL OF BACTERIOLOGY, 2014, 196 (18) :3289-3302

[60] Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut [J].

Heinken, Almut ;

Sahoo, Swagatika ;

Fleming, Ronan M. T. ;

Thiele, Ines .

GUT MICROBES, 2013, 4 (01) :28-40

← 1 2 3 4 5 6 7 8 9 10 →