Article (Scientific journals)
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas et al.
2019In Nature Protocols, 14 (3), p. 639-702
Peer Reviewed verified by ORBi
 

Files


Full Text
Heirendt et al., 2019.pdf
Author postprint (2.36 MB)
Download

All documents in ORBilu are protected by a user license.

Send to



Details



Abstract :
[en] 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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Heirendt, Laurent  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Arreckx, Sylvain
Pfau, Thomas ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Mendoza, Sebastian N.
Richelle, Anne
Heinken, Almut Katrin;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Haraldsdottir, Hulda S.
Wachowiak, Jacek
Keating, Sarah M.
Vlasov, Vanja ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Magnusdottir, Stefania
Ng, Chiam Yu
Preciat, German
Zagare, Alise ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Chan, Siu H. J.
Aurich, Maike K.
Clancy, Catherine M.
Modamio, Jennifer
Sauls, John T.
Noronha, Alberto ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Bordbar, Aarash
Cousins, Benjamin
El Assal, Diana Charles ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Valcarcel, Luis V.
Apaolaza, Inigo
Ghaderi, Susan ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
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.
Aragon Artacho, Francisco J.
Planes, Francisco J.
Stalidzans, Egils
Maass, Alejandro
Vempala, Santosh
Hucka, Michael
Saunders, Michael A.
Maranas, Costas D.
Lewis, Nathan E.
Sauter, Thomas ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Palsson, Bernhard O.
Thiele, Ines ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Fleming, Ronan M. T.
More authors (45 more) Less
External co-authors :
yes
Language :
English
Title :
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Publication date :
2019
Journal title :
Nature Protocols
ISSN :
1754-2189
eISSN :
1750-2799
Publisher :
Nature Publishing Group, United Kingdom
Volume :
14
Issue :
3
Pages :
639-702
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
Available on ORBilu :
since 02 April 2019

Statistics


Number of views
312 (79 by Unilu)
Number of downloads
125 (12 by Unilu)

Scopus citations®
 
584
Scopus citations®
without self-citations
497
OpenCitations
 
579
WoS citations
 
537

Bibliography


Similar publications



Contact ORBilu