Reference : Quantitative prediction of cellular metabolism with constraint-based models: the COBR...
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/16514
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
English
Schellenberger, Jan [> >]
Que, Richard [> >]
Fleming, Ronan MT mailto [> >]
Thiele, Ines mailto [> >]
Orth, Jeffrey D. [> >]
Feist, Adam M. [> >]
Zielinski, Daniel C. [> >]
Bordbar, Aarash [> >]
Lewis, Nathan E. [> >]
Rahmanian, Sorena [> >]
Kang, Joseph [> >]
Hyduke, Daniel R. [> >]
Palsson, Bernhard O. [> >]
2011
Nature Protocols
6
9
1290-1307
Yes
1754-2189
1750-2799
England
[en] Algorithms ; Computational Biology/methods ; Metabolic Networks and Pathways ; Software
[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.
http://hdl.handle.net/10993/16514
10.1038/nprot.2011.308

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Limited access
2011-Schellenberger-Quantitative prediction of cellular metabolism with constraint-based models- the COBRA Toolbox v2.0.pdfPublisher postprint1.12 MBRequest a copy

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.