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Protocols

COBRA Toolbox specifications

Information


Unique identifier OMICS_06004
Name COBRA Toolbox
Alternative name COnstraints Based Reconstruction and Analysis
Software type Framework/Library, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Fortran, MATLAB, Perl, Python, Julia
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Subtools


  • gMCS
  • Microbiome Modeling Toolbox

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Ines Thiele

Additional information


https://opencobra.github.io/cobratoolbox/stable/tutorials/index.html

Publications for COnstraints Based Reconstruction and Analysis

COBRA Toolbox citations

 (91)
library_books

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

2018
PLoS Genet
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] All simulations were performed in MATLAB 2017a (Mathworks) with scripts from the COBRA Toolbox (downloaded May 12, 2017 from the openCOBRA repository) [], and using the Gurobi 7.0.2 solver (gurobi.com), the SBMLToolbox 4.1.0 [], and libSBML 5.13.0 []. Boundary conditions for simul […]

library_books

Genome scale model driven strain design for dicarboxylic acid production in Yarrowia lipolytica

2018
BMC Syst Biol
PMCID: 5861505
PMID: 29560822
DOI: 10.1186/s12918-018-0542-5

[…] GDLS strain design algorithm [] was implemented in COBRA toolbox in Matlab, searching up to maximum of 5 knockout reactions with the outer objective of maximizing DDDA exchange flux. […]

library_books

Genome Scale, Constraint Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi

2018
mSystems
PMCID: 5864417
PMID: 29577088
DOI: 10.1128/mSystems.00170-17

[…] MatLab version 2014b (MathWorks, Inc.) running the Cobra Toolbox v3.0 (https://arxiv.org/abs/1710.04038) was used to integrate the set of differential equations describing the distribution and reaction network of N-containing compounds that results fr […]

library_books

Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach

2018
Sci Rep
PMCID: 5802761
PMID: 29410419
DOI: 10.1038/s41598-018-20574-z

[…] d,.An overview of the central metabolic pathways is shown in Fig.  (a detailed figure is provided as supplemental Figure ). We ran a set of in silico flux balance analysis (FBA) experiments using the COBRA toolbox to validate the stoichiometric completeness of the proposed metabolic network at all steps of the model development. Simulations for unconstrained network supported the direct coupling ( […]

call_split

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

2018
Nucleic Acids Res
PMCID: 5888115
PMID: 29394395
DOI: 10.1093/nar/gky069
call_split See protocol

[…] FBA analysis and MCMC sampling was performed with iJO1366 E. coli metabolic model (), COBRA Toolbox v2.0 () and COBRApy () as previously described (). In brief, the distribution of feasible fluxes for each reaction in the iJO1366 model was determined using Markov chain Monte Carlo (MCM […]

library_books

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

2018
PLoS One
PMCID: 5790215
PMID: 29381705
DOI: 10.1371/journal.pone.0189144

[…] ner information about cellular systemic characteristics (network-based pathway analysis []). All these different methods require a metabolic network model. We have used both COBRApy [] and the MATLAB COBRA Toolbox version 2.0.6 for the analyses described in this article []. […]

Citations

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COBRA Toolbox institution(s)
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg; Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden, Leiden, The Netherlands
COBRA Toolbox funding source(s)
Supported by the Luxembourg National Research Fund (FNR), through the ATTRACT programme (FNR/A12/01), and the OPEN grant (FNR/O16/11402054), as well as the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 757922).

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