The COBRA Toolbox
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The COBRA Toolbox
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Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
A
ACBSampler() (in module src.analysis.sampling.ACHR)
ACHRSampler() (in module src.analysis.sampling.ACHR)
ACHRSamplerParallelGeneral() (in module src.analysis.sampling.ACHR)
acidDissociationConstant() (in module src.analysis.thermo.reactantContribution)
acsendingAtomMaps() (in module src.dataIntegration.chemoInformatics)
adaptMacPath() (in module src.base.install)
adaptVMHDietToAGORA() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
addAnnotation() (in module src.visualization.cellDesigner)
addCOBRABinaryPathToSystemPath() (in module src.base.install)
addCOBRAConstraints() (in module src.reconstruction.refinement)
addCOBRAVariables() (in module src.reconstruction.refinement)
addColour() (in module src.visualization.cellDesigner)
addColourNode() (in module src.visualization.metabolicCartography)
addCouplingConstraint() (in module src.analysis.coupling)
addDemandReaction() (in module src.reconstruction.refinement)
addExchangeRxn() (in module src.reconstruction.refinement)
addFlux() (in module src.visualization.cellDesigner)
addFluxFBA() (in module src.visualization.metabolicCartography)
addFluxFBAdirectionAndColor() (in module src.visualization.metabolicCartography)
addGenes() (in module src.reconstruction.refinement)
addInchiToModel() (in module src.analysis.thermo.inchi)
addKeyToKnownHosts() (in module src.base.install)
addLoopLawConstraints() (in module src.analysis.thermo.thermoFBA)
addMetabolite() (in module src.reconstruction.refinement)
addmetabolites() (in module src.reconstruction.rBioNet)
addMetInfo() (in module src.reconstruction.comparison.modelBorgifier)
addMetInfoInCBmodel() (in module src.dataIntegration.chemoInformatics)
addMicrobeCommunityBiomass() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
addMiriam() (in module src.visualization.cellDesigner)
addMIRIAMAnnotations() (in module src.reconstruction.refinement)
addmissing() (in module src.reconstruction.rBioNet)
addMissingReactions() (in module src.analysis.rumba)
addMultipleMetabolites() (in module src.reconstruction.refinement)
addMultipleReactions() (in module src.reconstruction.refinement)
addMultipleReactionsIT() (in module src.reconstruction.refinement)
addNotes() (in module src.visualization.metabolicCartography)
addPseudoisomersToModel() (in module src.analysis.thermo.protons)
addRatioReaction() (in module src.analysis.coupling)
addReaction() (in module src.reconstruction.refinement)
addReactionGEM() (in module src.reconstruction.refinement)
addreactions() (in module src.reconstruction.rBioNet)
addSinkReactions() (in module src.reconstruction.refinement)
addSubSystemsToReactions() (in module src.reconstruction.refinement)
addThermoToModel() (in module src.analysis.thermo.componentContribution)
addToTmodel() (in module src.reconstruction.comparison.modelBorgifier)
adjustBaselinesInAlberty2006() (in module src.analysis.thermo.experimentalData.alberty2006)
alphabetizeModel() (in module src.reconstruction.refinement)
analyseObjectiveShadowPrices() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
analyseThermoConstrainedModel() (in module src.analysis.thermo.directionalityReport)
analyzeGCdesign() (in module src.design)
analyzeMgPipeResults() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
analyzeOptForceSol() (in module src.design.optForce)
analyzeOptKnock() (in module src.design)
analyzeRxns() (in module src.design)
analyzeSingleGeneDeletion() (in module src.dataIntegration.metabotools)
aprod() (in module src.analysis.subspaces.lsqr)
assignGPRA() (in module src.reconstruction.refinement)
assignQualDir() (in module src.analysis.thermo.directionalityReport)
assignRxnWeights() (in module src.reconstruction.fastGapFill.AuxillaryFiles)
assignSubSystems() (in module src.reconstruction.refinement)
assignThermoToModel() (in module src.analysis.thermo.groupContribution)
augmentBOF() (in module src.design)
autoMatchReactions() (in module src.reconstruction.comparison.modelBorgifier)
B
balancecheck() (in module src.reconstruction.rBioNet)
BalancePrep() (in module src.reconstruction.rBioNet)
BDCA() (in module src.base.solvers.varKin.BDCAmethods)
BDF() (in module src.base.solvers.varKin.derFreeMethods)
bilinearDecomposition() (in module src.analysis.topology.FR)
biomassPrecursorCheck() (in module src.analysis.exploration)
blocked() (in module src.dataIntegration.transcriptomics.SWIFTCORE)
boundsToFiles() (in module src.analysis.thermo.experimentalData)
buildAtomTransitionMultigraph() (in module src.dataIntegration.fluxomics.atomTransition)
buildAtomTransitionNetwork() (in module src.dataIntegration.fluxomics.atomTransition)
buildFluxDistLayout() (in module src.visualization.maps.ReconMap)
buildGmatrix() (in module src.analysis.gMCS)
buildLPproblemFromModel() (in module src.base.solvers)
buildMDFBAProblem() (in module src.analysis.mdFBA)
buildMTAproblemFromModel() (in module src.analysis.rMTA)
buildRxnEquations() (in module src.reconstruction.comparison.modelBorgifier)
buildRxnEquationsFromName() (in module src.reconstruction.comparison.modelBorgifier)
buildRxnGeneMat() (in module src.base.io.utilities)
,
[1]
buildTmodel() (in module src.reconstruction.comparison.modelBorgifier)
buildUFBAmodel() (in module src.analysis.uFBA)
C
C13ConfidenceInterval() (in module src.dataIntegration.fluxomics)
calcdGHT() (in module src.analysis.thermo.reactantContribution)
calcGroupStats() (in module src.base)
calcSampleDifference() (in module src.analysis.sampling)
calcSampleStats() (in module src.analysis.sampling)
calculateEPSILON() (in module src.analysis.rMTA)
calculateGeneKOMatrix() (in module src.analysis.rMTA)
calculateGeneMCS() (in module src.analysis.gMCS)
calculateInteractionsByTaxon() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
calculateLODs() (in module src.dataIntegration.metabotools)
calculateMCS() (in module src.analysis.gMCS)
calculateQuantitativeDiffs() (in module src.dataIntegration.metabotools)
calculateReactionAbundance() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
calculateReactionPresence() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
calculateSubsystemAbundance() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
canonicalRxn() (in module src.dataIntegration.chemoInformatics)
cdv2idv() (in module src.dataIntegration.fluxomics.c13solver)
cgls() (in module src.analysis.subspaces.lsqr)
changeCbMapOutput() (in module src.visualization.maps.ReconMap)
changeCOBRAConstraints() (in module src.reconstruction.refinement)
changeCOBRAVariable() (in module src.reconstruction.refinement)
changeGeneAssociation() (in module src.reconstruction.refinement)
changeMetColor() (in module src.visualization.metabolicCartography)
changeNodesArea() (in module src.visualization.metabolicCartography)
changeObjective() (in module src.analysis.FBA)
changeRxnBounds() (in module src.analysis.FBA)
changeRxnColorAndWidth() (in module src.visualization.metabolicCartography)
changeRxnMets() (in module src.reconstruction.refinement)
changeRxnType() (in module src.visualization.metabolicCartography)
charpos() (in module src.reconstruction.comparison.modelBorgifier)
checkBalance() (in module src.reconstruction.modelGeneration.massBalance)
checkCDerrors() (in module src.visualization.metabolicCartography)
checkCNAinstallation() (in module src.base.install)
checkCobraModelUnique() (in module src.reconstruction.modelGeneration)
checkDatabaseIDs() (in module src.reconstruction.modelGeneration.modelVerification)
checkDuplicateRxn() (in module src.reconstruction.modelGeneration)
checkEffectRxnKO() (in module src.dataIntegration.metabotools)
checkExchangeProfiles() (in module src.dataIntegration.metabotools)
checkFluxConsistency() (in module src.reconstruction.modelGeneration.fluxConsistency.GREEDY)
checkFormulaValidty() (in module src.reconstruction.modelGeneration.massBalance)
checkGeneMCS() (in module src.analysis.gMCS)
checkIDsForTypeExist() (in module src.reconstruction.refinement)
checkMassChargeBalance() (in module src.reconstruction.modelGeneration.massBalance)
checkMetIdsInModel() (in module src.dataIntegration.chemoInformatics)
checkModelPreFBA() (in module src.reconstruction.modelGeneration)
checkObjective() (in module src.reconstruction.modelGeneration)
checkPresentFields() (in module src.reconstruction.modelGeneration.modelVerification)
checkRankFR() (in module src.analysis.topology.FR)
checkScaling() (in module src.analysis.subspaces)
checkStoichiometricConsistency() (in module src.reconstruction.modelGeneration.stoichConsistency)
checkThermodynamicConsistency() (in module src.analysis.thermo.thermoFBA)
chrrExpSampler() (in module src.analysis.sampling.CHRR)
chrrParseModel() (in module src.analysis.sampling.CHRR)
chrrSampler() (in module src.analysis.sampling.CHRR)
classifyMoieties() (in module src.analysis.topology.conservedMoieties)
classifyRxns() (in module src.analysis.rumba)
cleanFilesFastFVA() (in module src.analysis.FVA.fastFVA)
cleanTmodel() (in module src.reconstruction.comparison.modelBorgifier)
closeGUI() (in module src.reconstruction.rBioNet)
cmpMet() (in module src.visualization.cellDesigner)
cmpRxn() (in module src.visualization.cellDesigner)
colorProtein() (in module src.visualization.metabolicCartography)
colorRxnsFromGenes() (in module src.visualization.metabolicCartography)
colorRxnType() (in module src.visualization.metabolicCartography)
colorSubsystemCD() (in module src.visualization.metabolicCartography)
colourAll() (in module src.visualization.cellDesigner)
colourNode() (in module src.visualization.cellDesigner)
colourNodeWhite() (in module src.visualization.cellDesigner)
colText() (in module src.reconstruction.comparison.modelBorgifier)
Combination() (in module src.dataIntegration.fluxomics.c13solver)
compareAllMets() (in module src.reconstruction.comparison.modelBorgifier)
compareBinsOfFluxes() (in module src.dataIntegration.fluxomics)
compareCbModels() (in module src.reconstruction.comparison.modelBorgifier)
compareConditions() (in module src.analysis.rumba)
compareMatricies() (in module src.reconstruction.comparison.modelBorgifier)
compareModelMapFormulas() (in module src.visualization.metabolicCartography)
compareModels() (in module src.reconstruction.comparison)
compareMultSamp() (in module src.dataIntegration.fluxomics)
compareSampleTraj() (in module src.analysis.sampling)
compareTwoMDVs() (in module src.dataIntegration.fluxomics)
compareTwoSamp() (in module src.dataIntegration.fluxomics)
compareTwoSamplesStat() (in module src.analysis.sampling)
compartment() (in module src.reconstruction.rBioNet)
computeElementalMatrix() (in module src.reconstruction.modelGeneration.massBalance)
computeFluxSplits() (in module src.dataIntegration.metabotools)
computeMetFormulae() (in module src.reconstruction.modelGeneration.massBalance)
computeMutualCoherence() (in module src.base.solvers.cardOpt.sparseLP)
computeParetoOptimality() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
computeRescuedGenes() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
conc2Rate() (in module src.dataIntegration.metabotools)
configureSetupThermoModelInputs() (in module src.analysis.thermo.vonBertalanffy)
connectedComponents() (in module src.analysis.topology)
connectedFR() (in module src.analysis.topology.FR)
connectedRxnsByEFM() (in module src.analysis.thermo.thermoFBA)
connectedRxnsInNullSpace() (in module src.analysis.thermo.thermoFBA)
conservationAnalysis() (in module src.analysis.subspaces)
consistentPotentials() (in module src.analysis.thermo.thermoFBA)
constrainRxnListAboveBound() (in module src.analysis.coupling)
constructElementalMatrix() (in module src.analysis.topology.conservedMoieties)
convertCbModelToCNAModel() (in module src.base.io)
convertCNAModelToCbModel() (in module src.base.io)
convertCobraLP2mps() (in module src.base.io)
convertGene2PathwayInteractions() (in module src.visualization.visualizeEpistasis)
convertHypergraphToBipartiteGraph() (in module src.analysis.topology.graphHypergraphConversion)
convertIrrevFluxDistribution() (in module src.reconstruction.refinement)
convertModelToEX() (in module src.base.io)
convertOldCouplingFormat() (in module src.base.io.utilities)
,
[1]
convertOldStyleModel() (in module src.base.io.utilities)
,
[1]
convertSBMLID() (in module src.base.io.utilities.SBML)
convertToIrreversible() (in module src.reconstruction.refinement)
convertToReversible() (in module src.reconstruction.refinement)
convRevSamples() (in module src.analysis.sampling.ACHR)
core() (in module src.dataIntegration.transcriptomics.SWIFTCORE)
correctMetName() (in module src.visualization.cellDesigner)
correctMetNameCD() (in module src.visualization.metabolicCartography)
correctRxnNameCD() (in module src.visualization.metabolicCartography)
correlateFluxWithTaxonAbundance() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
countC() (in module src.reconstruction.comparison.modelBorgifier)
coupleRxnList2Rxn() (in module src.analysis.coupling)
createBilevelMILPproblem() (in module src.design)
createColorsMap() (in module src.visualization.metabolicCartography)
createComputedSpeciesData() (in module src.analysis.thermo.groupContribution)
createDeltaMatchMatrix() (in module src.base)
createEmptyFields() (in module src.base.io.utilities)
,
[1]
CreateGPR() (in module src.reconstruction.rBioNet)
creategrRulesField() (in module src.base.io.utilities)
,
[1]
createHRWarmup() (in module src.analysis.sampling.ACHR)
createModel() (in module src.reconstruction.refinement)
createMultipleSpeciesModel() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
createPanModels() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
createPersonalizedModel() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
createTissueSpecificModel() (in module src.dataIntegration.transcriptomics)
createUniversalReactionModel() (in module src.base.io.KEGG)
createUniversalReactionModel2() (in module src.reconstruction.fastGapFill.AuxillaryFiles)
createXMatrix() (in module src.reconstruction.refinement)
createXMatrix2() (in module src.reconstruction.fastGapFill.AuxillaryFiles)
CSDF() (in module src.base.solvers.varKin.derFreeMethods)
cycleFreeFlux() (in module src.analysis.thermo.thermoFBA)
D
data2model() (in module src.reconstruction.rBioNet)
DBDF() (in module src.base.solvers.varKin.derFreeMethods)
DCA() (in module src.base.solvers.varKin.BDCAmethods)
decomposeMoietyVectors() (in module src.analysis.topology.conservedMoieties)
defaultColorCD() (in module src.visualization.metabolicCartography)
defaultLookMap() (in module src.visualization.metabolicCartography)
defineUptakeSecretionProfiles() (in module src.dataIntegration.metabotools)
deleteModelGenes() (in module src.analysis.deletion)
deleteProtons() (in module src.dataIntegration.chemoInformatics)
descFileRead() (in module src.base.io.definitions)
detectDeadEnds() (in module src.reconstruction.modelGeneration)
detectOutput() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
determineSignMatrix() (in module src.analysis.subspaces)
detMinSpan() (in module src.analysis.subspaces)
diffexprs2rxnFBS() (in module src.analysis.rMTA)
directionalityChangeReport() (in module src.analysis.thermo.directionalityReport)
directionalityStats() (in module src.analysis.thermo.directionalityReport)
directionalityStatsFigures() (in module src.analysis.thermo.directionalityReport)
dispStoichAsTable() (in module src.reconstruction.refinement)
doubleGeneDeletion() (in module src.analysis.deletion)
doubleProductionEnvelope() (in module src.design)
doubleRobustnessAnalysis() (in module src.analysis.robustnessAnalysis)
dynamicFBA() (in module src.analysis.dynamicFBA)
dynamicRFBA() (in module src.analysis.rFBA)
E
echelonNullspace() (in module src.analysis.subspaces.nullspace)
editChemicalFormula() (in module src.dataIntegration.chemoInformatics)
efmBackboneExtraction() (in module src.visualization.efmviz)
efmEnrichmentAnalysis() (in module src.visualization.efmviz)
efmFilter() (in module src.visualization.efmviz)
efmImport() (in module src.visualization.efmviz)
efmSubmodelExtractionAsSBML() (in module src.visualization.efmviz)
efmSubsystemsExtraction() (in module src.visualization.efmviz)
efmYieldAnalysis() (in module src.visualization.efmviz)
elementalMatrixToFormulae() (in module src.reconstruction.modelGeneration.massBalance)
enumerateOptimalSolutions() (in module src.analysis.FBA)
equivalentSets() (in module src.analysis.topology.extremeRays.lrs)
essentialRxn4MultipleModels() (in module src.analysis.exploration)
estimateDfGt0() (in module src.analysis.thermo.vonBertalanffy)
estimateDG_temp() (in module src.analysis.thermo.vonBertalanffy)
estimateDrGt0() (in module src.analysis.thermo.vonBertalanffy)
estimateMoietyFormulas() (in module src.analysis.topology.conservedMoieties)
evalObj() (in module src.base.solvers.cardOpt.sparseLP)
exportInputsMustOrder2ToGAMS() (in module src.design.optForceGAMS)
exportInputsMustToGAMS() (in module src.design.optForceGAMS)
exportInputsOptForceToGAMS() (in module src.design.optForceGAMS)
exportSetToGAMS() (in module src.design.optForceGAMS)
Extended_rate_function() (in module src.base.solvers.varKin.levMarMethods)
extendModelFieldsForType() (in module src.reconstruction.refinement)
extractCompModel() (in module src.reconstruction.refinement)
extractConditionSpecificModel() (in module src.dataIntegration.metabotools)
extractElementalTransitionNetwork() (in module src.dataIntegration.fluxomics.atomTransition)
extractFullRes() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
extractMetModel() (in module src.reconstruction.refinement)
extractSubNetwork() (in module src.reconstruction.refinement)
extractSubSysModel() (in module src.reconstruction.refinement)
extremePathways() (in module src.analysis.topology.extremeRays.lrs)
extremePools() (in module src.analysis.topology.extremeRays.lrs)
F
fastCalculateReactionAbundance() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
fastcc() (in module src.dataIntegration.transcriptomics.FASTCORE)
fastcc_nonconvex() (in module src.reconstruction.modelGeneration.fluxConsistency.DCA)
fastcore() (in module src.dataIntegration.transcriptomics.FASTCORE)
fastCoreWeighted() (in module src.dataIntegration.transcriptomics.FASTCORE)
fastFVA() (in module src.analysis.FVA.fastFVA)
fastGapFill() (in module src.reconstruction.fastGapFill)
fastLeakTest() (in module src.reconstruction.modelGeneration)
fastSetupCreator() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
fastSNP() (in module src.analysis.thermo.thermoFBA)
FEA() (in module src.analysis.fluxEnrichmentAnalysis)
findBlockedIrrRxns() (in module src.analysis.exploration)
findBlockedReaction() (in module src.analysis.exploration)
findCarbonRxns() (in module src.analysis.exploration)
findCyclicRxns() (in module src.analysis.topology)
findElementaryMoietyVectors() (in module src.analysis.topology.conservedMoieties)
findEpistaticInteractions() (in module src.analysis.exploration)
findExcRxns() (in module src.analysis.exploration)
findExtremePathway() (in module src.analysis.topology.extremeRays.optimalRays)
findExtremePool() (in module src.analysis.topology.extremeRays.optimalRays)
findFluxConsistentSubset() (in module src.reconstruction.modelGeneration.fluxConsistency)
findGeneIDs() (in module src.analysis.exploration)
findGenesFromRxns() (in module src.analysis.exploration)
findGPRFromRxns() (in module src.analysis.exploration)
findHiCarbonRxns() (in module src.analysis.exploration)
findIntracellularRxns() (in module src.reconstruction.fastGapFill.AuxillaryFiles)
findMassLeaksAndSiphons() (in module src.reconstruction.modelGeneration.stoichConsistency)
findMatchingFieldEntries() (in module src.analysis.exploration)
findMetabolicJunctions() (in module src.analysis.exploration)
findMetFromCompartment() (in module src.analysis.exploration)
findMetIDs() (in module src.analysis.exploration)
findMetMatch() (in module src.reconstruction.comparison.modelBorgifier)
findMetsFromCompartInMap() (in module src.visualization.metabolicCartography)
findMetsFromRxns() (in module src.analysis.exploration)
findMetsInMap() (in module src.visualization.metabolicCartography)
findMIIS() (in module src.analysis.findMIIS)
findMinCardModel() (in module src.dataIntegration.metabotools)
findMinimalLeakageMode() (in module src.reconstruction.modelGeneration.stoichConsistency)
findMinimalLeakageModeMet() (in module src.reconstruction.modelGeneration.stoichConsistency)
findMinimalLeakageModeRxn() (in module src.reconstruction.modelGeneration.stoichConsistency)
findMinNull() (in module src.analysis.thermo.thermoFBA)
findMustL() (in module src.design.optForce)
findMustLL() (in module src.design.optForce)
findMustLLWithGAMS() (in module src.design.optForceGAMS)
findMustLWithGAMS() (in module src.design.optForceGAMS)
findMustU() (in module src.design.optForce)
findMustUL() (in module src.design.optForce)
findMustULWithGAMS() (in module src.design.optForceGAMS)
findMustUU() (in module src.design.optForce)
findMustUUWithGAMS() (in module src.design.optForceGAMS)
findMustUWithGAMS() (in module src.design.optForceGAMS)
findNeighborRxns() (in module src.analysis.exploration)
findOptExchRxns() (in module src.dataIntegration.metabotools)
findOrphanRxns() (in module src.analysis.exploration)
findRootNPmets() (in module src.analysis.exploration)
findRxnFromCompartment() (in module src.analysis.exploration)
findRxnIDs() (in module src.analysis.exploration)
findRxnMatch() (in module src.reconstruction.comparison.modelBorgifier)
findRxnsActiveWithGenes() (in module src.analysis.exploration)
findRxnsFromCompartInMap() (in module src.visualization.metabolicCartography)
findRxnsFromGenes() (in module src.analysis.exploration)
findRxnsFromMets() (in module src.analysis.exploration)
findRxnsFromSubSystem() (in module src.analysis.exploration)
findRxnsInActiveWithGenes() (in module src.analysis.exploration)
findRxnsInMap() (in module src.visualization.metabolicCartography)
findRxnsPerTypeInMap() (in module src.visualization.metabolicCartography)
findSExRxnInd() (in module src.reconstruction.modelGeneration.massBalance)
findSparseMode() (in module src.dataIntegration.transcriptomics.FASTCORE)
findSparseModeWeighted() (in module src.dataIntegration.transcriptomics.FASTCORE)
findSparsePathway() (in module src.analysis.sparseFBA)
findStoichConsistentSubset() (in module src.reconstruction.modelGeneration.stoichConsistency)
findSubSysGen() (in module src.analysis.exploration)
findSubsystemOfGenes() (in module src.visualization.visualizeEpistasis)
findSubSystemsFromGenes() (in module src.analysis.exploration)
findTransRxns() (in module src.analysis.transport)
findTrspRxnFromMet() (in module src.analysis.exploration)
findUsedGenesLevels() (in module src.dataIntegration.transcriptomics.preprocessing)
fitC13Data() (in module src.dataIntegration.fluxomics)
fixChemFormulas() (in module src.reconstruction.comparison.modelBorgifier)
fixNames() (in module src.reconstruction.comparison.modelBorgifier)
flipRxnOrientation() (in module src.reconstruction.refinement)
fluxVariability() (in module src.analysis.FVA)
formula2mets() (in module src.reconstruction.rBioNet)
forwardProbablyReverseFigures() (in module src.analysis.thermo.directionalityReport)
forwardReversibleFigures() (in module src.analysis.thermo.directionalityReport)
forwardTransportQuantReverseFigures() (in module src.analysis.thermo.directionalityReport)
fourFundamentalSubpaces() (in module src.analysis.subspaces)
FuncGradHessSub() (in module src.base.solvers.varKin.BDCAmethods)
fvaJaccardIndex() (in module src.analysis.FVA)
FVAOptForce() (in module src.design.optForce)
G
gapFind() (in module src.reconstruction)
GDLS() (in module src.design)
generateChemicalDatabase() (in module src.dataIntegration.chemoInformatics)
generateCompactExchModel() (in module src.dataIntegration.metabotools)
generateFieldDescriptionFile() (in module src.base.io.utilities)
,
[1]
generateIsotopomerSolver() (in module src.dataIntegration.fluxomics.c13solver)
generateRules() (in module src.reconstruction.refinement)
generateSubsystemLayouts() (in module src.visualization.maps.ReconMap)
generateSubsytemsLayout() (in module src.visualization.maps.ReconMap)
generateSUXComp() (in module src.reconstruction.fastGapFill.AuxillaryFiles)
generateSUXMatrix() (in module src.reconstruction.fastGapFill)
generateSystemConfigReport() (in module src.base)
generateThermodynamicTables() (in module src.analysis.thermo.directionalityReport)
GenesAndReactions() (in module src.reconstruction.rBioNet)
GenesReactions() (in module src.reconstruction.rBioNet)
geometricFBA() (in module src.analysis.geometricFBA)
getAnnotationFieldName() (in module src.base.io.definitions)
getBinsOfFluxes() (in module src.dataIntegration.fluxomics)
getBioQualifiers() (in module src.base.io.utilities.SBML)
getCompareBinsOfFluxes() (in module src.dataIntegration.fluxomics)
getCompartment() (in module src.analysis.thermo.vonBertalanffy)
getCorrespondingCols() (in module src.analysis.topology)
getCorrespondingRows() (in module src.analysis.topology)
getDatabaseMappings() (in module src.base.io.utilities)
,
[1]
getDataBases() (in module src.base.io.utilities.SBML)
getDefaultCompartments() (in module src.base.io.utilities)
,
[1]
getDefaultCompartmentSymbols() (in module src.base.io.utilities)
,
[1]
getDefinedFieldProperties() (in module src.base.io.utilities)
,
[1]
getDistributedModel() (in module src.base.io.utilities)
,
[1]
getDistributedModelFolder() (in module src.base.io.utilities)
,
[1]
getElementalComposition() (in module src.reconstruction.modelGeneration.massBalance)
getEmptyConstraints() (in module src.reconstruction.refinement)
getFilesInDir() (in module src.base.install)
getgenelist() (in module src.reconstruction.rBioNet)
getGitBashVersion() (in module src.base.install)
getIDPositions() (in module src.reconstruction.refinement)
getIgnoredFiles() (in module src.base.install)
getIndividualSizeName() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
getMapMatrices() (in module src.visualization.metabolicCartography)
getMappingInfo() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
getMetAbbr() (in module src.reconstruction.refinement)
getMetaboliteMsDistr() (in module src.analysis.thermo.protons)
getMetabolitepKa() (in module src.analysis.thermo.protons)
getMIRIAMAnnotations() (in module src.analysis.exploration)
getModelFieldsForType() (in module src.reconstruction.refinement)
getModelSizes() (in module src.analysis.exploration)
getModelSubSystems() (in module src.analysis.exploration)
getMolecularWeight() (in module src.analysis.thermo.inchi)
getMultiDimensionFields() (in module src.base.io.utilities)
,
[1]
getMultiSpeciesModelId() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
getNullSpace() (in module src.analysis.subspaces.nullspace)
getObjectiveSense() (in module src.analysis.exploration)
GetOptGeneSol() (in module src.design)
getRandGlc() (in module src.dataIntegration.fluxomics)
getRankLUSOL() (in module src.analysis.subspaces.rank)
getRegisteredDatabases() (in module src.base.io.definitions)
GIMME() (in module src.dataIntegration.transcriptomics.GIMME)
GLM_FY() (in module src.base.solvers.varKin.levMarMethods)
GLM_YF() (in module src.base.solvers.varKin.levMarMethods)
gmscale() (in module src.analysis.subspaces)
goodInitialPoint() (in module src.dataIntegration.fluxomics)
GPR2Genes() (in module src.reconstruction.rBioNet)
GPR2models() (in module src.analysis.gMCS)
GPRparser() (in module src.dataIntegration.transcriptomics.preprocessing)
gpSampler() (in module src.analysis.sampling.ACHR)
greedyExtremePoolBasis() (in module src.analysis.topology.extremeRays.optimalRays)
growthExpMatch() (in module src.reconstruction.growthExpMatch)
guidedSim() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
H
hyperlink() (in module src.base)
I
identifyBlockedRxns() (in module src.reconstruction.fastGapFill)
identifyConservedMoieties() (in module src.analysis.topology.conservedMoieties)
identifyCorrelSets() (in module src.analysis.sampling)
identifyFastBlockedRxns() (in module src.analysis.exploration)
idv2cdv() (in module src.dataIntegration.fluxomics.c13solver)
idv2idv() (in module src.dataIntegration.fluxomics.c13solver)
idv2mdv() (in module src.dataIntegration.fluxomics.c13solver)
illustrate_ppp() (in module src.dataIntegration.metabotools)
iMAT() (in module src.dataIntegration.transcriptomics.iMAT)
inchi2mol() (in module src.analysis.thermo.inchi)
INIT() (in module src.dataIntegration.transcriptomics.INIT)
initFBAFields() (in module src.base.io.utilities)
,
[1]
InitialBDCA() (in module src.base.solvers.varKin.BDCAmethods)
InitialDuplo() (in module src.base.solvers.varKin.derFreeMethods)
Initialization() (in module src.base.solvers.varKin.levMarMethods)
initMgPipe() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
installDevTools() (in module src.base.install)
installGitBash() (in module src.base.install)
integerizeS() (in module src.analysis.topology)
integrateGeneExpressionData() (in module src.dataIntegration.metabotools)
intergrate() (in module src.visualization.cellDesigner)
isCompatible() (in module src.base.solvers)
ismatlab() (in module src.reconstruction.comparison.modelBorgifier)
isotopomerViewer() (in module src.dataIntegration.fluxomics)
ispolymer() (in module src.reconstruction.modelGeneration.massBalance)
isReactionInSubSystem() (in module src.analysis.exploration)
isSameCobraModel() (in module src.reconstruction.refinement)
J
joinModelsPairwiseFromList() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
K
Keep_reactions() (in module src.reconstruction.rBioNet)
keepCompartment() (in module src.reconstruction.refinement)
KLDis() (in module src.analysis.KLdistance)
KLdistance() (in module src.analysis.KLdistance)
L
largestConnectedFR() (in module src.analysis.topology.FR)
leakTest() (in module src.reconstruction.modelGeneration.stoichConsistency)
LegalRxnFormula() (in module src.reconstruction.rBioNet)
LevMar() (in module src.base.solvers.varKin.levMarMethods)
lin_sym_solver_mldivide() (in module src.base.solvers.varKin.levMarMethods)
linearMOMA() (in module src.analysis.MOMA)
linearROOM() (in module src.analysis.ROOM)
listBiGGModels() (in module src.base.io.BiGG)
LLM() (in module src.base.solvers.varKin.levMarMethods)
LMLS() (in module src.base.solvers.varKin.levMarMethods)
LMTR() (in module src.base.solvers.varKin.levMarMethods)
load_reaction() (in module src.reconstruction.rBioNet)
loadBiGGModel() (in module src.base.io.BiGG)
loadIdentifiedModel() (in module src.base.io.utilities)
,
[1]
LoadReaction() (in module src.reconstruction.rBioNet)
loadSamples() (in module src.analysis.sampling)
loadUncModels() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
LP10() (in module src.dataIntegration.transcriptomics.FASTCORE)
LP10cvx() (in module src.dataIntegration.transcriptomics.FASTCORE)
LP3() (in module src.dataIntegration.transcriptomics.FASTCORE)
LP7() (in module src.dataIntegration.transcriptomics.FASTCORE)
lrsInputHalfspace() (in module src.analysis.topology.extremeRays.lrs.lrsInterface)
lrsOutputReadRay() (in module src.analysis.topology.extremeRays.lrs.lrsInterface)
lsqr() (in module src.analysis.subspaces.lsqr)
lsqraprod() (in module src.analysis.subspaces.lsqr)
lsqrtest() (in module src.analysis.subspaces.lsqr)
M
make3Dplot() (in module src.dataIntegration.metabotools)
makeDummyModel() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
makeFRresultsTable() (in module src.analysis.topology.FR)
makeNamesUnique() (in module src.reconstruction.comparison.modelBorgifier)
makeSBMLAnnotationString() (in module src.base.io.utilities.SBML)
makeSummaryModels() (in module src.dataIntegration.metabotools)
makeViolinPlots() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
mapAnnotationsToFields() (in module src.base.io.utilities.SBML)
mapExpressionToReactions() (in module src.dataIntegration.transcriptomics.preprocessing)
mapFormula() (in module src.visualization.metabolicCartography)
mapKEGGID2Model() (in module src.base.io.KEGG)
mapMatch() (in module src.reconstruction.comparison.modelBorgifier)
mapMetName2KEGGID() (in module src.base.io.KEGG)
matrixCoherence() (in module src.analysis.topology)
maxCardinalityConservationVector() (in module src.reconstruction.modelGeneration.stoichConsistency)
maxEntConsVector() (in module src.reconstruction.modelGeneration.stoichConsistency)
maxstar() (in module src.analysis.thermo.utilities)
MBA() (in module src.dataIntegration.transcriptomics.MBA)
mdFBA() (in module src.analysis.mdFBA)
mergeModelFieldPositions() (in module src.reconstruction.refinement)
mergeModelsBorg() (in module src.reconstruction.comparison.modelBorgifier)
mergeTextDataAndData() (in module src.base.io.utilities)
,
[1]
mergeTrxns() (in module src.reconstruction.comparison.modelBorgifier)
mergeTwoModels() (in module src.reconstruction.refinement)
met_charge_formula() (in module src.reconstruction.rBioNet)
metaboliteMassBalancePlot() (in module src.analysis.thermo.thermoFBA)
metabolites_in_database() (in module src.reconstruction.rBioNet)
metCompare() (in module src.reconstruction.comparison.modelBorgifier)
metCompareGUI() (in module src.reconstruction.comparison.modelBorgifier)
mets2str() (in module src.reconstruction.rBioNet)
mgPipe() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
mgSimResCollect() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
microbiotaModelSimulator() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
minCardinalityConservationRelaxationVector() (in module src.reconstruction.modelGeneration.stoichConsistency)
minimizeModelFlux() (in module src.analysis.FBA)
mixFraction() (in module src.analysis.sampling.ACHR)
mkTableOfAddedExchanges() (in module src.dataIntegration.metabotools)
model2data() (in module src.reconstruction.rBioNet)
model2text() (in module src.reconstruction.rBioNet)
model2xls() (in module src.base.io.utilities)
,
[1]
model_description() (in module src.reconstruction.rBioNet)
model_stats() (in module src.reconstruction.rBioNet)
modifyReactionsMetabolites() (in module src.visualization.metabolicCartography)
mol2inchi() (in module src.analysis.thermo.inchi)
moleFraction() (in module src.analysis.thermo.protons)
moleFractionStats() (in module src.analysis.thermo.protons)
molFilesToCDFfile() (in module src.analysis.thermo.molFiles)
MOMA() (in module src.analysis.MOMA)
moveRxn() (in module src.reconstruction.refinement)
MTA() (in module src.analysis.rMTA)
MTA_MIQP() (in module src.analysis.rMTA)
MTA_TS() (in module src.analysis.rMTA)
mtFVA() (in module src.analysis.FVA)
multiProductionEnvelope() (in module src.design)
multiProductionEnvelopeInorg() (in module src.design)
N
naturallabel() (in module src.dataIntegration.fluxomics)
neighborRxn2data() (in module src.reconstruction.rBioNet)
networkTopology() (in module src.dataIntegration.metabotools)
newCompsNewMets() (in module src.reconstruction.comparison.modelBorgifier)
normalizeCoverage() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
normalizePoints() (in module src.analysis.rumba)
nullspaceLUSOLapply2Modes() (in module src.analysis.subspaces.nullspace)
nullSpaceOperator() (in module src.analysis.subspaces.nullspace)
nullSpaceOperatorApply() (in module src.analysis.subspaces.nullspace)
numAtomsOfElementInFormula() (in module src.reconstruction.modelGeneration.massBalance)
O
obtainAtomMappingsRDT() (in module src.dataIntegration.chemoInformatics)
obtainMetStructures() (in module src.dataIntegration.chemoInformatics)
optForce() (in module src.design.optForce)
optForceWithGAMS() (in module src.design.optForceGAMS)
optGene() (in module src.design)
optGeneFitness() (in module src.design)
optGeneFitnessTilt() (in module src.design)
optimalConservationVectors() (in module src.reconstruction.modelGeneration.stoichConsistency)
optimalScores() (in module src.reconstruction.comparison.modelBorgifier)
optimizeCardinality() (in module src.base.solvers.cardOpt.sparseLP)
optimizeCbModel() (in module src.analysis.FBA)
optimizeRegModel() (in module src.analysis.rFBA)
optimizeTwoCbModels() (in module src.base.solvers)
optimizeVKmodel() (in module src.base.solvers.varKin)
OptKnock() (in module src.design)
optWeightExp() (in module src.reconstruction.comparison.modelBorgifier)
optWeightLin() (in module src.reconstruction.comparison.modelBorgifier)
orderModelFields() (in module src.reconstruction.refinement)
orderModelFieldsBorg() (in module src.reconstruction.comparison.modelBorgifier)
organizeModelCool() (in module src.reconstruction.comparison.modelBorgifier)
outputHypergraph() (in module src.base.io.utilities)
,
[1]
outputNetworkCytoscape() (in module src.base.io.utilities)
,
[1]
outputNetworkOmix() (in module src.base.io.utilities)
,
[1]
P
parsave() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
parseBoolean() (in module src.base)
parseCD() (in module src.visualization.cellDesigner)
parseCobraVarargin() (in module src.base)
parseCVTerms() (in module src.base.io.utilities.SBML)
parseGPR() (in module src.base)
parseMetNames() (in module src.base)
parseRxnFormula() (in module src.base)
parseSBMLAnnotationField() (in module src.base.io.utilities)
,
[1]
parseSBMLAnnotationFieldRxn() (in module src.base.io.utilities)
,
[1]
parseSBMLNotesField() (in module src.base.io.utilities)
,
[1]
partition() (in module src.dataIntegration.transcriptomics.SWIFTCORE)
performPPP() (in module src.dataIntegration.metabotools)
performSampling() (in module src.dataIntegration.metabotools)
performStatisticalAnalysis() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
pFBA() (in module src.analysis.parsimoniousFBA)
pHbalanceProtons() (in module src.reconstruction.modelGeneration.massBalance)
phenotypePhasePlane() (in module src.analysis.robustnessAnalysis)
planariseModel() (in module src.base.io.utilities)
,
[1]
plotActivityCoefficients() (in module src.analysis.thermo.protons)
plotEssentialRxns() (in module src.analysis.exploration)
plotFeasibleReactionEnergyRanges() (in module src.analysis.thermo.directionalityReport)
plotFluxesAgainstOrganismAbundances() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
plotFRresults() (in module src.analysis.topology.FR)
plotHistConv() (in module src.analysis.sampling)
plotMappingInfo() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
plotMoleFraction() (in module src.analysis.thermo.protons)
plotSampleHist() (in module src.analysis.sampling)
portableGitSetup() (in module src.base.install)
position() (in module src.visualization.cellDesigner)
postMINERVArequest() (in module src.visualization.maps.ReconMap)
postProcessGapFillSolutions() (in module src.reconstruction.fastGapFill)
predictFluxSplits() (in module src.dataIntegration.metabotools)
predictMicrobeContributions() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis)
prepareFastGapFill() (in module src.reconstruction.fastGapFill)
prepareTest() (in module src.base.install)
preparseGPR() (in module src.base)
prepIntegrationQuant() (in module src.dataIntegration.metabotools)
printConstraints() (in module src.analysis.exploration)
printDirectionalityFromBounds() (in module src.analysis.thermo.thermoFBA)
printFluxBounds() (in module src.analysis.exploration)
printFluxVector() (in module src.analysis.exploration)
printFRdependencies() (in module src.analysis.topology.FR)
printGPRForRxns() (in module src.analysis.exploration)
printInRecon3Dmap() (in module src.visualization.maps.ReconMap)
printLabeledData() (in module src.analysis.exploration)
printMatrix() (in module src.analysis.exploration)
printMinimalLeakageMode() (in module src.reconstruction.modelGeneration.stoichConsistency)
printRxnFormula() (in module src.analysis.exploration)
printSampleStats() (in module src.analysis.sampling)
printSolutionGEM() (in module src.reconstruction.growthExpMatch)
printUptakeBound() (in module src.analysis.exploration)
printUptakeBoundCom() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
priorityKeqMeasurement() (in module src.analysis.thermo.experimentalDesign)
processingLLCs() (in module src.analysis.thermo.thermoFBA)
productionEnvelope() (in module src.design)
projectOntoSubspace() (in module src.analysis.subspaces.subspaceProjection)
projectSVD() (in module src.analysis.subspaces.subspaceProjection)
pruneModel() (in module src.dataIntegration.metabotools)
pValDistForModelOverlap() (in module src.analysis.rumba)
R
randomKO() (in module src.design)
randomObjFBASol() (in module src.analysis.FBA)
Rate_function() (in module src.base.solvers.varKin.BDCAmethods)
(in module src.base.solvers.varKin.derFreeMethods)
Rate_function1() (in module src.base.solvers.varKin.levMarMethods)
rBioNet_search() (in module src.reconstruction.rBioNet)
rBioNetAbout() (in module src.reconstruction.rBioNet)
rBioNetSaveLoad() (in module src.reconstruction.rBioNet)
rBioNetSettings() (in module src.reconstruction.rBioNet)
ReactionChecks() (in module src.reconstruction.rBioNet)
reactionCompare() (in module src.reconstruction.comparison.modelBorgifier)
reactionCompareGUI() (in module src.reconstruction.comparison.modelBorgifier)
ReactionEq() (in module src.reconstruction.rBioNet)
readAtomMappingFromRxnFile() (in module src.dataIntegration.chemoInformatics)
readBooleanRegModel() (in module src.base.io.utilities)
,
[1]
readCbModel() (in module src.base.io)
readCbTmodel() (in module src.reconstruction.comparison.modelBorgifier)
readCD() (in module src.visualization.cellDesigner)
readMetRxnBoundsFiles() (in module src.analysis.thermo.experimentalData)
readMinosSolution() (in module src.base.io)
readMixedData() (in module src.base.io)
readSBML() (in module src.base.io.utilities)
,
[1]
readSimPhenyCMPD() (in module src.base.io.utilities)
,
[1]
readSimPhenyGPR() (in module src.base.io.utilities)
,
[1]
readSimPhenyGprText() (in module src.base.io.utilities)
,
[1]
realpH() (in module src.analysis.thermo.protons)
reassignFwBwMatch() (in module src.reconstruction.refinement)
rebuildModel() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
ReconstructionCreator() (in module src.reconstruction.rBioNet)
ReconstructionTool() (in module src.reconstruction.rBioNet)
reduceModel() (in module src.reconstruction.refinement)
regulariseModelFormulae() (in module src.reconstruction.modelGeneration.massBalance)
relaxedFBA() (in module src.analysis.relaxedFBA)
relaxFBA_cappedL1() (in module src.analysis.relaxedFBA)
removeCDReactions() (in module src.visualization.metabolicCartography)
removeCOBRAConstraints() (in module src.reconstruction.refinement)
removeCorrelRxns() (in module src.analysis.sampling.ACHR)
removeDeadEnds() (in module src.reconstruction.modelGeneration)
removeDuplicateNames() (in module src.reconstruction.comparison.modelBorgifier)
removeFieldEntriesForType() (in module src.reconstruction.refinement)
removeGenesFromModel() (in module src.reconstruction.refinement)
removeMapMol() (in module src.visualization.metabolicCartography)
removeMapReactions() (in module src.visualization.metabolicCartography)
removeMapSpecies() (in module src.visualization.metabolicCartography)
removeMapSpeciesOnly() (in module src.visualization.metabolicCartography)
removeMetabolites() (in module src.reconstruction.refinement)
removeProblematicCharacters() (in module src.reconstruction.comparison.modelBorgifier)
removeRxns() (in module src.reconstruction.refinement)
removeSubSystemsFromRxns() (in module src.reconstruction.refinement)
removeTempFiles() (in module src.base.install)
removeTrivialStoichiometry() (in module src.reconstruction.refinement)
removeUnusedGenes() (in module src.reconstruction.refinement)
renameDREAMOutputFiles() (in module src.dataIntegration.fluxomics.atomTransition)
repairXML() (in module src.visualization.cellDesigner)
reporterMets() (in module src.base)
representativeMoiety() (in module src.analysis.topology.conservedMoieties)
representativeMolecule() (in module src.analysis.topology.conservedMoieties)
restrictModelsToFields() (in module src.base.io.utilities)
,
[1]
retrieveMet() (in module src.visualization.cellDesigner)
retrieveModelStats() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
rMTA() (in module src.analysis.rMTA)
rMTAsaveInExcel() (in module src.analysis.rMTA)
robustnessAnalysis() (in module src.analysis.robustnessAnalysis)
robustnessAnalysisWB() (in module src.analysis.robustnessAnalysis)
ROOM() (in module src.analysis.ROOM)
rowReduce() (in module src.analysis.subspaces.rowReduce)
rowvector() (in module src.reconstruction.comparison.modelBorgifier)
rumba() (in module src.analysis.rumba)
runHiLoExp() (in module src.dataIntegration.fluxomics)
S
sampleCbModel() (in module src.analysis.sampling)
sampleScatterMatrix() (in module src.analysis.sampling)
saveInputsMustSetsFirstOrder() (in module src.design.optForce)
saveInputsMustSetsSecondOrder() (in module src.design.optForce)
saveInputsOptForce() (in module src.design.optForce)
sbmlTestModelToMat() (in module src.base.io)
scaleSMatrix() (in module src.analysis.subspaces)
score_KS() (in module src.dataIntegration.fluxomics)
score_ridge() (in module src.dataIntegration.fluxomics)
scoreC13Fit() (in module src.dataIntegration.fluxomics.c13solver)
searchModel() (in module src.analysis.exploration)
selectGeneFromGPR() (in module src.dataIntegration.transcriptomics.preprocessing)
selMatrix() (in module src.base)
setCommonZeroStandardGibbsEnergyOfFormation() (in module src.analysis.thermo.reactantContribution)
setConstraintsIrrevModel() (in module src.reconstruction.modelGeneration)
setConstraintsOnBiomassReaction() (in module src.dataIntegration.metabotools)
setMediumConstraints() (in module src.dataIntegration.metabotools)
setQualitativeConstraints() (in module src.dataIntegration.metabotools)
setQuantConstraints() (in module src.dataIntegration.metabotools)
setRxnSubSystems() (in module src.reconstruction.refinement)
setSemiQuantConstraints() (in module src.dataIntegration.metabotools)
setupComponentContribution() (in module src.analysis.thermo.componentContribution)
setupThermoModel() (in module src.analysis.thermo.vonBertalanffy)
setWorkerCount() (in module src.base)
sim_general() (in module src.reconstruction.rBioNet)
similarities() (in module src.reconstruction.rBioNet)
similarity() (in module src.reconstruction.rBioNet)
simpleOptKnock() (in module src.design)
simulatePairwiseInteractions() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
singleGeneDeletion() (in module src.analysis.deletion)
singleMetaboliteSpeciesReaction() (in module src.analysis.thermo.reactantContribution)
singleMetaboliteThermoFigure() (in module src.analysis.thermo.directionalityReport)
singleProductionEnvelope() (in module src.design)
singleRxnDeletion() (in module src.analysis.deletion)
solveBooleanRegModel() (in module src.analysis.rFBA)
solveCobraLP() (in module src.base.solvers)
solveCobraMILP() (in module src.base.solvers)
solveCobraMIQP() (in module src.base.solvers)
solveCobraQP() (in module src.base.solvers)
sortRDTfiles() (in module src.dataIntegration.chemoInformatics)
sparseFBA() (in module src.analysis.sparseFBA)
sparseLP() (in module src.base.solvers.cardOpt.sparseLP)
splitString() (in module src.base)
src.analysis (module)
src.analysis.coupling (module)
src.analysis.deletion (module)
src.analysis.dynamicFBA (module)
src.analysis.exploration (module)
src.analysis.FBA (module)
src.analysis.findMIIS (module)
src.analysis.fluxEnrichmentAnalysis (module)
src.analysis.FVA (module)
src.analysis.FVA.fastFVA (module)
src.analysis.geometricFBA (module)
src.analysis.gMCS (module)
src.analysis.KLdistance (module)
src.analysis.mdFBA (module)
src.analysis.MOMA (module)
src.analysis.multiSpecies (module)
src.analysis.multiSpecies.microbiomeModelingToolbox (module)
src.analysis.multiSpecies.microbiomeModelingToolbox.additionalAnalysis (module)
src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe (module)
src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling (module)
src.analysis.multiSpecies.SteadyCom (module)
src.analysis.multiSpecies.SteadyCom.subroutines (module)
src.analysis.parsimoniousFBA (module)
src.analysis.relaxedFBA (module)
src.analysis.rFBA (module)
src.analysis.rMTA (module)
src.analysis.robustnessAnalysis (module)
src.analysis.ROOM (module)
src.analysis.rumba (module)
src.analysis.sampling (module)
src.analysis.sampling.ACHR (module)
src.analysis.sampling.CHRR (module)
src.analysis.sparseFBA (module)
src.analysis.subspaces (module)
src.analysis.subspaces.lsqr (module)
src.analysis.subspaces.nullspace (module)
src.analysis.subspaces.rank (module)
src.analysis.subspaces.rowReduce (module)
src.analysis.subspaces.subspaceProjection (module)
src.analysis.thermo (module)
src.analysis.thermo.componentContribution (module)
src.analysis.thermo.directionalityReport (module)
src.analysis.thermo.experimentalData (module)
src.analysis.thermo.experimentalData.alberty2006 (module)
src.analysis.thermo.experimentalDesign (module)
src.analysis.thermo.groupContribution (module)
src.analysis.thermo.inchi (module)
src.analysis.thermo.molFiles (module)
src.analysis.thermo.protons (module)
src.analysis.thermo.reactantContribution (module)
src.analysis.thermo.thermoFBA (module)
src.analysis.thermo.transport (module)
src.analysis.thermo.utilities (module)
src.analysis.thermo.vonBertalanffy (module)
src.analysis.topology (module)
src.analysis.topology.conservedMoieties (module)
src.analysis.topology.extremeRays (module)
src.analysis.topology.extremeRays.lrs (module)
src.analysis.topology.extremeRays.lrs.lrsInterface (module)
src.analysis.topology.extremeRays.optimalRays (module)
src.analysis.topology.FR (module)
src.analysis.topology.graphHypergraphConversion (module)
src.analysis.transport (module)
src.analysis.uFBA (module)
src.base (module)
src.base.install (module)
src.base.io (module)
src.base.io.BiGG (module)
src.base.io.definitions (module)
src.base.io.KEGG (module)
src.base.io.utilities (module)
,
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src.base.io.utilities.SBML (module)
src.base.solvers (module)
src.base.solvers.cardOpt (module)
src.base.solvers.cardOpt.sparseLP (module)
src.base.solvers.varKin (module)
src.base.solvers.varKin.BDCAmethods (module)
src.base.solvers.varKin.derFreeMethods (module)
src.base.solvers.varKin.levMarMethods (module)
src.dataIntegration.chemoInformatics (module)
src.dataIntegration.fluxomics (module)
src.dataIntegration.fluxomics.atomTransition (module)
src.dataIntegration.fluxomics.c13solver (module)
src.dataIntegration.metabotools (module)
src.dataIntegration.transcriptomics (module)
src.dataIntegration.transcriptomics.FASTCORE (module)
src.dataIntegration.transcriptomics.GIMME (module)
src.dataIntegration.transcriptomics.iMAT (module)
src.dataIntegration.transcriptomics.INIT (module)
src.dataIntegration.transcriptomics.MBA (module)
src.dataIntegration.transcriptomics.preprocessing (module)
src.dataIntegration.transcriptomics.SWIFTCORE (module)
src.design (module)
src.design.optForce (module)
src.design.optForceGAMS (module)
src.reconstruction (module)
src.reconstruction.comparison (module)
src.reconstruction.comparison.modelBorgifier (module)
src.reconstruction.fastGapFill (module)
src.reconstruction.fastGapFill.AuxillaryFiles (module)
src.reconstruction.growthExpMatch (module)
src.reconstruction.modelGeneration (module)
src.reconstruction.modelGeneration.fluxConsistency (module)
src.reconstruction.modelGeneration.fluxConsistency.DCA (module)
src.reconstruction.modelGeneration.fluxConsistency.GREEDY (module)
src.reconstruction.modelGeneration.massBalance (module)
src.reconstruction.modelGeneration.modelVerification (module)
src.reconstruction.modelGeneration.stoichConsistency (module)
src.reconstruction.rBioNet (module)
src.reconstruction.refinement (module)
src.visualization (module)
src.visualization.cellDesigner (module)
src.visualization.efmviz (module)
src.visualization.maps (module)
src.visualization.maps.ReconMap (module)
src.visualization.metabolicCartography (module)
src.visualization.visualizeEpistasis (module)
standardGibbsFormationEnergyStats() (in module src.analysis.thermo.directionalityReport)
standardiseMolDatabase() (in module src.dataIntegration.chemoInformatics)
statisticsAddedExchanges() (in module src.dataIntegration.metabotools)
SteadyCom() (in module src.analysis.multiSpecies.SteadyCom)
SteadyComCplex() (in module src.analysis.multiSpecies.SteadyCom.subroutines)
SteadyComFVA() (in module src.analysis.multiSpecies.SteadyCom)
SteadyComFVAgr() (in module src.analysis.multiSpecies.SteadyCom.subroutines)
SteadyComPOA() (in module src.analysis.multiSpecies.SteadyCom)
SteadyComPOAgr() (in module src.analysis.multiSpecies.SteadyCom.subroutines)
SteadyComSubroutines() (in module src.analysis.multiSpecies.SteadyCom.subroutines)
StopCritBDCA() (in module src.base.solvers.varKin.BDCAmethods)
StopCritDuplo() (in module src.base.solvers.varKin.derFreeMethods)
StopCriterion() (in module src.base.solvers.varKin.levMarMethods)
submitGapFill() (in module src.reconstruction.fastGapFill)
subspaceProjector() (in module src.analysis.subspaces.subspaceProjection)
subspaceSVD() (in module src.analysis.subspaces.subspaceProjection)
summarizeSamplingResults() (in module src.dataIntegration.metabotools)
surfNet() (in module src.analysis.exploration)
swiftcc() (in module src.dataIntegration.transcriptomics.SWIFTCORE)
swiftcore() (in module src.dataIntegration.transcriptomics.SWIFTCORE)
swiftGapFill() (in module src.reconstruction.fastGapFill)
T
test4HumanFctExt() (in module src.reconstruction.modelGeneration)
testATPYieldFromCsources() (in module src.reconstruction.modelGeneration)
testForTypeIIIPathways() (in module src.analysis.topology)
testOptKnockSol() (in module src.design)
testPathway() (in module src.reconstruction)
theoretMaxProd() (in module src.design)
thermodynamicAdjustmentToStoichiometry() (in module src.analysis.thermo.reactantContribution)
TmodelFields() (in module src.reconstruction.comparison.modelBorgifier)
TmodelStats() (in module src.reconstruction.comparison.modelBorgifier)
transformFullMap2XML() (in module src.visualization.metabolicCartography)
transformFullXML2Map() (in module src.visualization.metabolicCartography)
transformKEGG2Model() (in module src.base.io.KEGG)
transformMap2XML() (in module src.visualization.metabolicCartography)
transformModel2KEGG() (in module src.base.io.KEGG)
transformToIrreversibleMap() (in module src.visualization.metabolicCartography)
transformToReversibleMap() (in module src.visualization.metabolicCartography)
transformXML2Map() (in module src.visualization.metabolicCartography)
translateList() (in module src.base)
translateMetagenome2AGORA() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe)
transportReactionBool() (in module src.analysis.thermo.transport)
transportRxnAM() (in module src.dataIntegration.chemoInformatics)
U
unbalanced() (in module src.reconstruction.rBioNet)
unifyMetabolicMapCD() (in module src.visualization.metabolicCartography)
unifyMetabolicPPImapCD() (in module src.visualization.metabolicCartography)
updateCD() (in module src.visualization.cellDesigner)
updateCobraToolbox() (in module src.base.install)
updateFieldOrderForType() (in module src.reconstruction.refinement)
updateGenes() (in module src.reconstruction.refinement)
updateGitBash() (in module src.base.install)
updateMetNames() (in module src.reconstruction.refinement)
updateObj() (in module src.base.solvers.cardOpt.sparseLP)
useDiet() (in module src.analysis.multiSpecies.microbiomeModelingToolbox.pairwiseInteractionModeling)
V
verifyCobraProblem() (in module src.base.solvers)
verifyModel() (in module src.reconstruction.modelGeneration.modelVerification)
verifyModelBorg() (in module src.reconstruction.comparison.modelBorgifier)
verifyPoints() (in module src.analysis.sampling.ACHR)
verifyRuleSyntax() (in module src.reconstruction.modelGeneration.modelVerification)
visualizePathwayInEpistasis() (in module src.visualization.visualizeEpistasis)
W
webDatabases() (in module src.reconstruction.rBioNet)
webKeggMapper() (in module src.reconstruction.rBioNet)
write4ti2() (in module src.base.io.utilities)
,
[1]
writeCbModel() (in module src.base.io)
writeCD() (in module src.visualization.cellDesigner)
writeCytoscapeEdgeAttributeTable() (in module src.base.io.utilities)
,
[1]
writeGDXFromCOBRA() (in module src.base.io)
writeLPProblem() (in module src.base.io)
writeMinosProblem() (in module src.base.io)
writePajekNet() (in module src.base.io.utilities)
,
[1]
writeReactionListThermo() (in module src.analysis.thermo.directionalityReport)
writeRxnfile() (in module src.dataIntegration.chemoInformatics)
writeSBML() (in module src.base.io.utilities)
,
[1]
writeText2XML() (in module src.visualization.cellDesigner)
writeTXT() (in module src.visualization.cellDesigner)
writeXML() (in module src.visualization.cellDesigner)
X
xls2model() (in module src.base.io.utilities)
,
[1]