A Beginner’s Guide to the COBRA Toolbox

Abstract Motivation Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account. Results We developed DEMETER, a COBRA Toolbox extension, that enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data, and refinement of pathways based on manually refined genome annotations. Availability DEMETER and tutorials are freely available at https://github.com/opencobra.

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Correction: BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases

Molecular BioSystems ◽

10.1039/c6mb90040b ◽

2016 ◽

Vol 12 (12) ◽

pp. 3743-3743

Author(s):

Oveis Jamialahmadi ◽

Ehsan Motamedian ◽

Sameereh Hashemi-Najafabadi

Keyword(s):

Cobra Toolbox

Correction for ‘BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases’ by Oveis Jamialahmadi et al., Mol. BioSyst., 2016, DOI: 10.1039/c6mb00532b.

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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Nature Protocols ◽

10.1038/s41596-018-0098-2 ◽

2019 ◽

Vol 14 (3) ◽

pp. 639-702 ◽

Cited By ~ 184

Author(s):

Laurent Heirendt ◽

Sylvain Arreckx ◽

Thomas Pfau ◽

Sebastián N. Mendoza ◽

Anne Richelle ◽

...

Keyword(s):

Cobra Toolbox ◽

Constraint Based Models

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MOFA: Multi-Objective Flux Analysis for the COBRA Toolbox

10.1101/2021.05.20.445041 ◽

2021 ◽

Author(s):

Marc Griesemer ◽

Ali Navid

Keyword(s):

Flux Analysis ◽

E Coli ◽

Multi Objective ◽

Trade Offs ◽

Quantitative Examination ◽

Genome Scale ◽

Cobra Toolbox ◽

Normalized Normal Constraint ◽

Constraint Based Models ◽

Biological Organisms

Multi-objective Optimization (MO) is an important tool for quantitative examination of the trade-offs faced by biological organisms. Using genome-scale constraint-based models of metabolism (GSMs),Multi-Objective Flux Analysis (MOFA) allows MO analyses of trade-offs among key biological tasks. The leading software package for conducting a plethora of different types of constraint-based analyses using GSMs is the COBRA Toolbox for MATLAB. We have developed a new add-on tool for this toolbox using Normalized Normal Constraint (NNC) that performs MOFA for a number of objectives only limited by computation power (n≤10). This development will facilitate MOFA analyses by COBRA's large user base and allow greater multi-faceted examination of metabolic trade-offs in complicated biological systems. Availability and Implementation: The MOFA software is freely available for download from https://bbs.llnl.gov under the GPL v2 license. The program runs on MATLAB with the COBRA software on Windows, Linux, and MacOS. It includes a detailed manual explaining the input and output of a simulation, a listing of the code's functions, and an example MOFA run using a well-curated GSM model of E. coli.

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The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

10.1101/318485 ◽

2018 ◽

Cited By ~ 2

Author(s):

Federico Baldini ◽

Almut Heinken ◽

Laurent Heirendt ◽

Stefania Magnusdottir ◽

Ronan M.T. Fleming ◽

...

Keyword(s):

Microbial Communities ◽

Microbial Interactions ◽

Microbial Genome ◽

Metagenomic Data ◽

Link Type ◽

Metabolic Interactions ◽

Constraint Based Modeling ◽

Genome Scale ◽

Cobra Toolbox

MotivationThe application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.ResultsTo address this shortage, we created a comprehensive toolbox to model i) microbe-microbe and host-microbe metabolic interactions, and ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the COBRA Toolbox.AvailabilityThe Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

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