Description: 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.
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File list (Check if you may need any files):
cobra\addLoopLawConstraints.m
.....\analyzeRxns.m
.....\changeGeneAssociation.m
.....\CHANGELOG
.....\changeObjective.m
.....\changeRxnBounds.m
.....\changeRxnMets.m
.....\checkCobraModelUnique.m
.....\checkDuplicateRxn.m
.....\checkObjective.m
.....\computeElementalMatrix.m
.....\computeMW.m
.....\convertIrrevFluxDistribution.m
.....\convertModelToEX.m
.....\convertToIrreversible.m
.....\convertToReversible.m
.....\deleteModelGenes.m
.....\..sign\alphabetizeModel.m
.....\......\analyzeGCdesign.m
.....\......\analyzeOptKnock.m
.....\......\augmentBOF.m
.....\......\createBilevelMILPproblem.m
.....\......\doubleProductionEnvelope.m
.....\......\findCarbonRxns.m
.....\......\findHiCarbonRxns.m
.....\......\GDLS.m
.....\......\GetOptGeneSol.m
.....\......\multiProductionEnvelope.m
.....\......\multiProductionEnvelopeInorg.m
.....\......\optGene.m
.....\......\optGeneFitness.m
.....\......\optGeneFitnessTilt.m
.....\......\OptKnock.m
.....\......\randomKO.m
.....\......\setConstraintsIrrevModel.m
.....\......\simpleOptKnock.m
.....\......\testOptKnockSol.m
.....\......\theoretMaxProd.m
.....\detectDeadEnds.m
.....\.ocs\alpha.png
.....\....\c++.png
.....\....\c.png
.....\....\.obra\addLoopLawConstraints.html
.....\....\.....\analyzeRxns.html
.....\....\.....\changeGeneAssociation.html
.....\....\.....\changeObjective.html
.....\....\.....\changeRxnBounds.html
.....\....\.....\changeRxnMets.html
.....\....\.....\checkCobraModelUnique.html
.....\....\.....\checkDuplicateRxn.html
.....\....\.....\checkMassChargeBalance.html
.....\....\.....\checkObjective.html
.....\....\.....\computeElementalMatrix.html
.....\....\.....\computeMW.html
.....\....\.....\convertIrrevFluxDistribution.html
.....\....\.....\convertModelToEX.html
.....\....\.....\convertToIrreversible.html
.....\....\.....\convertToReversible.html
.....\....\.....\deleteModelGenes.html
.....\....\.....\..sign\alphabetizeModel.html
.....\....\.....\......\analyzeGCdesign.html
.....\....\.....\......\analyzeOptKnock.html
.....\....\.....\......\augmentBOF.html
.....\....\.....\......\createBilevelMILPproblem.html
.....\....\.....\......\doubleProductionEnvelope.html
.....\....\.....\......\findCarbonRxns.html
.....\....\.....\......\findHiCarbonRxns.html
.....\....\.....\......\GDLS.html
.....\....\.....\......\GetOptGeneSol.html
.....\....\.....\......\menu.html
.....\....\.....\......\multiProductionEnvelope.html
.....\....\.....\......\multiProductionEnvelopeInorg.html
.....\....\.....\......\optGene.html
.....\....\.....\......\optGeneFitness.html
.....\....\.....\......\optGeneFitnessTilt.html
.....\....\.....\......\OptKnock.html
.....\....\.....\......\randomKO.html
.....\....\.....\......\setConstraintsIrrevModel.html
.....\....\.....\......\simpleOptKnock.html
.....\....\.....\......\testOptKnockSol.html
.....\....\.....\......\theoretMaxProd.html
.....\....\.....\detectDeadEnds.html
.....\....\.....\doubleGeneDeletion.html
.....\....\.....\doubleRobustnessAnalysis.html
.....\....\.....\dynamicFBA.html
.....\....\.....\enumerateOptimalSolutions.html
.....\....\.....\.xternal\addpath_recurse.html
.....\....\.....\........\BuildMPS\BuildMPS.html
.....\....\.....\........\........\menu.html
.....\....\.....\........\........\SaveMPS.html
.....\....\.....\........\errobar_plus.html
.....\....\.....\........\ezimplot3.html
.....\....\.....\........\m2html\m2html.html
.....\....\.....\........\......\mdot.html
.....\....\.....\........\......\menu.html
.....\....\.....\........\menu.html
.....\....\.....\........\sparseNull.html
.....\....\.....\extractCompModel.html
.....\....\.....\extractMetModel.html
.....\....\.....\extractSubNetwork.html
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