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

By Scott A. Becker, Adam M. Feist, Monica L. Mo, Gregory Hannum, Bernhard O. Palsson, Markus J. Herrgård. Nature Protocols, 2007

874 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7a8e2c1098c7b4fee3086567b58d23135d5928b4

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Citations in the corpus

A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, methodology): “Sample installation instructions for the lp_solve LP solver on Windows can be found in Becker et al. 16 .”
Environments that Induce Synthetic Microbial Ecosystems (2010, methodology): “Models were imported into Matlab from the XML files using the Cobra toolbox [25].”
Computationally efficient flux variability analysis (2010, methodology): “The running times are given in Table 2 where fastFVA is compared to the direct implementation of FVA found in the COBRA toolbox [10].”
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007, methodology): “The system was represented in the form of a stoichiometric matrix (see Materials and methods) and utilized in the available software platforms SimPheny, and LINDO or TOMLAB in conjunction with MATLAB (Becker et al, 2007).”
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0 (2019, methodology): “101 Procedure [4] fails when running contribute Your local changes are not yet published (committed) Follow procedure [3] of the contribute menu in order to publish your changes first as explained in Step 100”
Systems Biology of Cancer Metastasis (2019, methodology): “Reconstructed genetic regulatory networks (Ahmad et al., 2012; Liang et al., 2012; Walsh et al., 2017) Ability to integrate large scale and sometimes multimodal experimental data Limited to transciptomic processes, ignoring metabolic and proteomic regulation Whole cell metabolic network modeling (Ag”
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 (2011, methodology): “The iJO1366 model was exported from SimPheny as an SBML file and the COBRAToolbox (Becker et al, 2007), a Matlab (The MathWorks Inc., Natick, MA) Toolbox, was used for additional model testing.”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “Other biological constraints, such as regulation or capacity constraints, may also prevent the organism from using optimal ﬂux distributions (Oliveira et al ., 2005; Feist et al ., 2007).”
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints (2017, methodology): “Both GECKO and ecYeast7 are compatible with the COBRA toolbox (Schellenberger et al, 2011) or any constraint-based approach.”
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis (2010, methodology): “The COBRA toolbox (43) was used to load and optimize”
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor (2018, methodology): “As such, the RAVEN toolbox has functioned as one of the two major MATLAB-based packages for constraint-based metabolic modelling, together with the COBRA Toolbox [23–25].”
Applications of genome-scale metabolic reconstructions (2009, methodology): “reconstructions”
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum (2013, methodology): “The native model format for the RAVEN Toolbox follows the format of the yeast consensus metabolic network [27], but models in the COBRA Toolbox format can also be imported [21].”
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010, methodology): “…function of the BiGG knowledgebase is exporting reconstructions as Systems Biology Markup Language (SBML) files [46], which are specifically designed to work with the Matlab COBRA toolbox [47] and Systems Biology Research Tool [48] for performing Legend flux balance analysis and other computations.”