The COnstraint-Based Reconstruction and Analysis Toolbox

Version 3.0.4 (219 MB) by laurentheirendt
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
3.7
(3)
4K Downloads
Updated 1 Feb 2024
View License on GitHub

The COnstraint-Based Reconstruction and Analysis Toolbox is a MATLAB software suite for quantitative prediction of cellular and multicellular biochemical networks with constraint-based modelling. It implements a comprehensive collection of basic and advanced modelling methods, including reconstruction and model generation as well as biased and unbiased model-driven analysis methods.

It is widely used for modelling, analysing and predicting a variety of metabolic phenotypes using genome-scale biochemical networks.

-- Manuscript available under doi.org/10.1038/s41596-018-0098-2

Cite As

Laurent Heirendt & Sylvain Arreckx, Thomas Pfau, Sebastian N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdottir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdottir, Chiam Yu Ng, German Preciat, Alise Zagare, Siu H.J. Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto Noronha, Aarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Inigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Miguel A.P. Oliveira, Phan T. Vuong, Lemmer P. El Assal, Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Francisco J. Aragon Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard Ø. Palsson, Ines Thiele, Ronan M.T. Fleming, Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0, Nature Protocols, volume 14, pages 639–702, 2019 doi.org/10.1038/s41596-018-0098-2.

MATLAB Release Compatibility
Created with R2018b
Compatible with R2014b and later releases
Platform Compatibility
Windows macOS Linux
Categories
Find more on Statistics and Machine Learning Toolbox in Help Center and MATLAB Answers

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

.artenolis

deprecated

deprecated/_cardOpt_tangiCode

deprecated/_directionalityReport_old

deprecated/_fluxomics_obsolete

deprecated/_io_depreciated

deprecated/_maps_old

deprecated/_maps_old/tools

deprecated/_modelManipulationOri

deprecated/_testDependencyStructure

deprecated/_thermo_old_data

deprecated/_topology/FR

docs/source/guides

docs/source/installation

docs/source/modules

external/analysis

external/analysis/RAVEN

external/analysis/StoichTools

external/analysis/graph_analysis

external/analysis/lnbin

external/analysis/mptoolbox

external/analysis/mptoolbox/@mp

external/analysis/mptoolbox/@mp/private

external/analysis/plotConfMat

external/analysis/totallyUnimodular

external/base/install

external/base/io

external/base/io/BuildMPS

external/base/io/json

external/base/io/libSBML-5.19-matlab

external/base/io/pdb2mat_v1.1

external/base/io/xlwrite

external/base/solvers/glpkmex

external/base/solvers/lusolMex32bit

external/base/utilities

external/base/utilities/NearestSymmetricPositiveDefinite

external/base/utilities/append_pdfs

external/base/utilities/cellstructeq

external/base/utilities/codeConsistency

external/base/utilities/datastructure

external/base/utilities/dependencyAnalyzer

external/base/utilities/findjobj

external/base/utilities/grep

external/base/utilities/histogram_distance

external/base/utilities/m2html

external/base/utilities/m2html/@template

external/base/utilities/m2html/@template/private

external/base/utilities/m2html/private

external/base/utilities/matrixcomp

external/base/utilities/programStatistics

external/base/utilities/rdir

external/base/utilities/sloc

external/base/utilities/slocDir

external/base/utilities/slocstat

external/base/utilities/textprogressbar

external/base/utilities/vennX

external/base/utilities/violinPlots

external/dataIntegration/mCADRE

external/visualization

external/visualization/barvalues

external/visualization/crameri

external/visualization/distinguishable_colors

external/visualization/gscatter3b

external/visualization/labelpoints

external/visualization/linspecer

external/visualization/plotregion

external/visualization/spyc

external/visualization/venn

external/visualization/venn4

src/analysis/FBA

src/analysis/FVA

src/analysis/FVA/fastFVA

src/analysis/FVA/fastFVA/mex

src/analysis/GT1

src/analysis/KLdistance

src/analysis/LT1

src/analysis/LT2

src/analysis/MOMA

src/analysis/QFCA

src/analysis/ROOM

src/analysis/calculateFluxShifts

src/analysis/coupling

src/analysis/deletion

src/analysis/deletion/Syntheticlethals/Fast-SL

src/analysis/dynamicFBA

src/analysis/exploration

src/analysis/exploration/surfNetSubfunctions

src/analysis/fastForest

src/analysis/filterNonFluxReactions

src/analysis/filterRateLimittingReactions

src/analysis/findMIIS

src/analysis/findUpDownRegulatedGenes

src/analysis/fluxEnrichmentAnalysis

src/analysis/gMCS

src/analysis/geometricFBA

src/analysis/mdFBA

src/analysis/multiSpecies/SteadyCom

src/analysis/multiSpecies/SteadyCom/subroutines

src/analysis/multiSpecies/microbiomeModelingToolbox/additionalAnalysis

src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe

src/analysis/multiSpecies/microbiomeModelingToolbox/pairwiseInteractionModeling

src/analysis/nutritionAlgorithm

src/analysis/parsimoniousFBA

src/analysis/percentileCalc

src/analysis/rFBA

src/analysis/rMTA

src/analysis/relaxedFBA

src/analysis/robustnessAnalysis

src/analysis/rumba

src/analysis/sampling

src/analysis/sampling/ACHR

src/analysis/sampling/BarrierRound

src/analysis/sampling/BarrierRound/CMatrix

src/analysis/sampling/BarrierRound/CMatrix/coverage

src/analysis/sampling/BarrierRound/CMatrix/include

src/analysis/sampling/BarrierRound/PolytopeSimplifier

src/analysis/sampling/BarrierRound/PolytopeSimplifier/coverage

src/analysis/sampling/BarrierRound/utils

src/analysis/sampling/CHRR

src/analysis/sparseFBA

src/analysis/subspaces

src/analysis/subspaces/lsqr

src/analysis/subspaces/nullspace

src/analysis/subspaces/rank

src/analysis/subspaces/rowReduce

src/analysis/subspaces/subspaceProjection

src/analysis/thermo/componentContribution

src/analysis/thermo/componentContribution/new

src/analysis/thermo/componentContribution/old

src/analysis/thermo/directionalityReport

src/analysis/thermo/directionalityReport/old

src/analysis/thermo/experimentalData

src/analysis/thermo/experimentalData/alberty2006

src/analysis/thermo/experimentalDesign

src/analysis/thermo/findThermoConsistentFluxSubset

src/analysis/thermo/formulae

src/analysis/thermo/groupContribution

src/analysis/thermo/groupContribution/jankowski

src/analysis/thermo/groupContribution/new

src/analysis/thermo/groupContribution/old

src/analysis/thermo/groupContribution/wang

src/analysis/thermo/inchi

src/analysis/thermo/inchi/new

src/analysis/thermo/inchi/old

src/analysis/thermo/molFiles

src/analysis/thermo/molFiles/new

src/analysis/thermo/molFiles/old

src/analysis/thermo/optCardThermo

src/analysis/thermo/protons

src/analysis/thermo/protons/new

src/analysis/thermo/protons/old

src/analysis/thermo/reactantContribution

src/analysis/thermo/thermoDirectionality

src/analysis/thermo/thermoFBA

src/analysis/thermo/trainingModel

src/analysis/thermo/trainingModel/new

src/analysis/thermo/trainingModel/old

src/analysis/thermo/transport

src/analysis/thermo/utilities

src/analysis/thermo/vonBertalanffy

src/analysis/topology

src/analysis/topology/FR

src/analysis/topology/conservedMoieties

src/analysis/topology/conservedMoieties/old

src/analysis/topology/extremeRays/lrs

src/analysis/topology/extremeRays/lrs/lrsInterface

src/analysis/topology/extremeRays/optimalRays

src/analysis/topology/graphHypergraphConversion

src/analysis/transport

src/analysis/uFBA

src/analysis/wholeBody/Nutrition_Modelling_Toolbox

src/analysis/wholeBody/PSCMToolbox

src/analysis/wholeBody/PSCMToolbox/BMRcalculations

src/analysis/wholeBody/PSCMToolbox/hostMicrobeInteraction

src/analysis/wholeBody/PSCMToolbox/io

src/analysis/wholeBody/PSCMToolbox/setConstraints

src/analysis/wholeBody/PSCMToolbox/setConstraints/diets

src/analysis/wholeBody/PSCMToolbox/setConstraints/organWeight

src/base

src/base/ci

src/base/codeConsistency

src/base/install

src/base/io

src/base/io/BiGG

src/base/io/KEGG

src/base/io/definitions

src/base/io/json

src/base/io/newt

src/base/io/old

src/base/io/python

src/base/io/python/cobrapy

src/base/io/python/condalab

src/base/io/python/pyPath

src/base/io/python/tmp

src/base/io/utilities

src/base/io/utilities/SBML

src/base/paths

src/base/solvers

src/base/solvers/NLP

src/base/solvers/cardOpt/smoothConcave

src/base/solvers/cardOpt/sparseLP

src/base/solvers/cardOpt/sparseLP/old

src/base/solvers/cplex

src/base/solvers/entropicFBA

src/base/solvers/gams

src/base/solvers/getSetSolver

src/base/solvers/init

src/base/solvers/lindo

src/base/solvers/lp_solve

src/base/solvers/msk

src/base/solvers/param

src/base/solvers/rescale

src/base/solvers/varKin

src/base/solvers/varKin/BDCAmethods

src/base/solvers/varKin/derFreeMethods

src/base/solvers/varKin/levMarMethods

src/base/utilities

src/chatGPT/MatGPT/helpers

src/dataIntegration

src/dataIntegration/XomicsToModel

src/dataIntegration/XomicsToModel/analysis

src/dataIntegration/XomicsToModel/metabolomics

src/dataIntegration/XomicsToModel/oneRxnPerActiveGene

src/dataIntegration/XomicsToModel/prepareData

src/dataIntegration/XomicsToModel/proteomics

src/dataIntegration/XomicsToModel/thermoKernel

src/dataIntegration/XomicsToModel/thermoKernel/thermoQP

src/dataIntegration/chemoInformatics

src/dataIntegration/chemoInformatics/RXN

src/dataIntegration/chemoInformatics/RXN/old

src/dataIntegration/chemoInformatics/inchi

src/dataIntegration/chemoInformatics/metabolites

src/dataIntegration/chemoInformatics/molecularWeight

src/dataIntegration/chemoInformatics/molecularWeight/basicPhysicochemicalData

src/dataIntegration/chemoInformatics/reactions

src/dataIntegration/fluxomics