Article (Scientific journals)
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Schellenberger, Jan; Que, Richard; Fleming, Ronan MT et al.
2011In Nature Protocols, 6 (9), p. 1290-1307
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Keywords :
Algorithms; Computational Biology/methods; Metabolic Networks and Pathways; Software
Abstract :
[en] Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a substantial update of this in silico toolbox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis methods developed since its original release. New functions include (i) network gap filling, (ii) (13)C analysis, (iii) metabolic engineering, (iv) omics-guided analysis and (v) visualization. As with the first version, the COBRA Toolbox reads and writes systems biology markup language-formatted models. In version 2.0, we improved performance, usability and the level of documentation. A suite of test scripts can now be used to learn the core functionality of the toolbox and validate results. This toolbox lowers the barrier of entry to use powerful COBRA methods.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Schellenberger, Jan
Que, Richard
Fleming, Ronan MT 
Thiele, Ines 
Orth, Jeffrey D.
Feist, Adam M.
Zielinski, Daniel C.
Bordbar, Aarash
Lewis, Nathan E.
Rahmanian, Sorena
Kang, Joseph
Hyduke, Daniel R.
Palsson, Bernhard O.
More authors (3 more) Less
External co-authors :
yes
Language :
English
Title :
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Publication date :
2011
Journal title :
Nature Protocols
ISSN :
1754-2189
eISSN :
1750-2799
Publisher :
Nature Publishing Group, United Kingdom
Volume :
6
Issue :
9
Pages :
1290-1307
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
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