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PMID: 21886097 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Nature protocols ·Vol. 6 ·No. 9 ·2011-08-04 ·Pages 1290-307

Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ

Abstract

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.

MeSH Terms
Algorithms Computational Biology/methods Metabolic Networks and Pathways Software
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Schellenberger Jan
Bioinformatics Program, University of California San Diego, La Jolla, California, USA.
Que Richard
Fleming Ronan M T
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 Ø
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Article Info
Journal
Nature protocols
Abbr.
Nat Protoc
ISSN
1750-2799
DOI
10.1038/nprot.2011.308
Published
2011-08-04
Epub
2011-00-04
Pages
1290-307
Language
English
Region
England
NLM ID
101284307
PMCID
PMC3319681
Subset
IM
Grants
NIGMS NIH HHS · R01 GM057089-11S1 · United States
NIAID NIH HHS · Y1-AI-8401-01 · United States
NIGMS NIH HHS · R01 GM068837-05A1 · United States
NIGMS NIH HHS · GM057089-11S1 · United States
NIGMS NIH HHS · R01 GM057089 · United States
NIGMS NIH HHS · R01 GM057089-12 · United States
NIGMS NIH HHS · R01 GM068837 · United States
NIGMS NIH HHS · GM68837-05A1 · United States
NIAID NIH HHS · Y01 AI008401 · United States
External Links
PubMed source DOI: 10.1038/nprot.2011.308 PMC Full Text View journal details
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