Index

• PhysiCellModelManager.AbstractMonad
• PhysiCellModelManager.AbstractPhysiCellSequence
• PhysiCellModelManager.AbstractPopulationTimeSeries
• PhysiCellModelManager.AbstractSampling
• PhysiCellModelManager.AbstractTrial
• PhysiCellModelManager.AbstractVariation
• PhysiCellModelManager.AddGridVariationsResult
• PhysiCellModelManager.AddLHSVariationsResult
• PhysiCellModelManager.AddRBDVariationsResult
• PhysiCellModelManager.AddSobolVariationsResult
• PhysiCellModelManager.AddVariationMethod
• PhysiCellModelManager.AddVariationsResult
• PhysiCellModelManager.AgentDict
• PhysiCellModelManager.AgentID
• PhysiCellModelManager.AverageSubstrateTimeSeries
• PhysiCellModelManager.CoVariation
• PhysiCellModelManager.ColumnSetup
• PhysiCellModelManager.CopyOrMove
• PhysiCellModelManager.DiscreteVariation
• PhysiCellModelManager.DistributedVariation
• PhysiCellModelManager.ElementaryVariation
• PhysiCellModelManager.ExtracellularSubstrateTimeSeries
• PhysiCellModelManager.GSAMethod
• PhysiCellModelManager.GSASampling
• PhysiCellModelManager.GridVariation
• PhysiCellModelManager.ImportDestFolder
• PhysiCellModelManager.ImportDestFolders
• PhysiCellModelManager.ImportSource
• PhysiCellModelManager.ImportSources
• PhysiCellModelManager.InputFolder
• PhysiCellModelManager.InputFolders
• PhysiCellModelManager.LHSVariation
• PhysiCellModelManager.LatentVariation
• PhysiCellModelManager.MOAT
• PhysiCellModelManager.MOATSampling
• PhysiCellModelManager.Monad
• PhysiCellModelManager.MonadPopulationTimeSeries
• PhysiCellModelManager.PCMMGlobals
• PhysiCellModelManager.PCMMMissingProject
• PhysiCellModelManager.PCMMOutput
• PhysiCellModelManager.PCMMPCFResult
• PhysiCellModelManager.ParsedVariations
• PhysiCellModelManager.PhysiCellComponent
• PhysiCellModelManager.PhysiCellSequence
• PhysiCellModelManager.PhysiCellSnapshot
• PhysiCellModelManager.ProjectLocations
• PhysiCellModelManager.PruneOptions
• PhysiCellModelManager.RBD
• PhysiCellModelManager.RBDSampling
• PhysiCellModelManager.RBDVariation
• PhysiCellModelManager.Sampling
• PhysiCellModelManager.Simulation
• PhysiCellModelManager.SimulationPopulationTimeSeries
• PhysiCellModelManager.SimulationProcess
• PhysiCellModelManager.SobolPCMM
• PhysiCellModelManager.SobolSampling
• PhysiCellModelManager.SobolVariation
• PhysiCellModelManager.Sobolʼ
• PhysiCellModelManager.Trial
• PhysiCellModelManager.VariationID
• PhysiCellModelManager.VoxelWeights
• PhysiCellModelManager.XMLPath
• Base.run
• Base.run
• Base.run
• Distributions.cdf
• PairCorrelationFunction.pcf
• PhysiCellModelManager.NormalDistributedVariation
• PhysiCellModelManager.UniformDistributedVariation
• PhysiCellModelManager._connectedComponents
• PhysiCellModelManager._createTrial
• PhysiCellModelManager._loadCells!
• PhysiCellModelManager._loadGraph!
• PhysiCellModelManager._loadMesh!
• PhysiCellModelManager._loadSubstrates!
• PhysiCellModelManager._motilityStatistics
• PhysiCellModelManager.abstractSamplingForeignReferenceSubSchema
• PhysiCellModelManager.adaptConfig
• PhysiCellModelManager.adaptCustomCPP
• PhysiCellModelManager.adaptCustomCode
• PhysiCellModelManager.adaptCustomHeader
• PhysiCellModelManager.adaptCustomModules
• PhysiCellModelManager.adaptMain
• PhysiCellModelManager.adaptMakefile
• PhysiCellModelManager.adaptProject
• PhysiCellModelManager.addAttackRateVariationDimension!
• PhysiCellModelManager.addCDFVariations
• PhysiCellModelManager.addColumns
• PhysiCellModelManager.addCustomDataVariationDimension!
• PhysiCellModelManager.addDomainVariationDimension!
• PhysiCellModelManager.addFolderNameColumns!
• PhysiCellModelManager.addMacro
• PhysiCellModelManager.addMacrosIfNeeded
• PhysiCellModelManager.addPhysiECMIfNeeded
• PhysiCellModelManager.addRoadRunnerIfNeeded
• PhysiCellModelManager.addSimulationID
• PhysiCellModelManager.addVariationRow
• PhysiCellModelManager.addVariationRows
• PhysiCellModelManager.addVariations
• PhysiCellModelManager.apoptosisPath
• PhysiCellModelManager.appendVariations
• PhysiCellModelManager.assembleIntracellular!
• PhysiCellModelManager.assertInitialized
• PhysiCellModelManager.attackPath
• PhysiCellModelManager.attackRatePath
• PhysiCellModelManager.attackRatesPath
• PhysiCellModelManager.averageExtracellularSubstrate
• PhysiCellModelManager.averageSubstrate
• PhysiCellModelManager.baseToExecutable
• PhysiCellModelManager.buildWhereClause
• PhysiCellModelManager.calculateGSA!
• PhysiCellModelManager.cellDataSequence
• PhysiCellModelManager.cellDefinitionPath
• PhysiCellModelManager.cellInteractionsPath
• PhysiCellModelManager.cellLabels
• PhysiCellModelManager.cellParameterName
• PhysiCellModelManager.cellPositionsForPCF
• PhysiCellModelManager.cellTypeToNameDict
• PhysiCellModelManager.centralDB
• PhysiCellModelManager.cleanUpStudioInputs
• PhysiCellModelManager.collectSimulationTasks
• PhysiCellModelManager.columnName
• PhysiCellModelManager.columnNameToXMLPath
• PhysiCellModelManager.columnsExist
• PhysiCellModelManager.commitHashToTagDict
• PhysiCellModelManager.compilerFlags
• PhysiCellModelManager.compressIDs
• PhysiCellModelManager.computeVoxelIndices
• PhysiCellModelManager.computeVoxelSubscripts
• PhysiCellModelManager.configPath
• PhysiCellModelManager.connectedComponents
• PhysiCellModelManager.constituentIDs
• PhysiCellModelManager.constituentType
• PhysiCellModelManager.constituentTypeFilename
• PhysiCellModelManager.constructSelectQuery
• PhysiCellModelManager.copyFilesToFolders
• PhysiCellModelManager.createComponentDestFilename
• PhysiCellModelManager.createDefaultGitIgnore
• PhysiCellModelManager.createDefaultStatusCodesTable
• PhysiCellModelManager.createExportFolder
• PhysiCellModelManager.createICCellXMLTemplate
• PhysiCellModelManager.createICECMXMLTemplate
• PhysiCellModelManager.createInputFolder!
• PhysiCellModelManager.createInputFolders!
• PhysiCellModelManager.createInputsTOMLTemplate
• PhysiCellModelManager.createPCMMTable
• PhysiCellModelManager.createProject
• PhysiCellModelManager.createSchema
• PhysiCellModelManager.createSortedRBDMatrix
• PhysiCellModelManager.createTrial
• PhysiCellModelManager.createXMLFile
• PhysiCellModelManager.currentPhysiCellVersionID
• PhysiCellModelManager.customDataPath
• PhysiCellModelManager.cyclePath
• PhysiCellModelManager.dataDir
• PhysiCellModelManager.databaseDiagnostics
• PhysiCellModelManager.deathPath
• PhysiCellModelManager.defaultJobOptions
• PhysiCellModelManager.defaultLatentParameterNames
• PhysiCellModelManager.deleteAllSimulations
• PhysiCellModelManager.deleteMonad
• PhysiCellModelManager.deleteSampling
• PhysiCellModelManager.deleteSimulation
• PhysiCellModelManager.deleteSimulations
• PhysiCellModelManager.deleteSimulationsByStatus
• PhysiCellModelManager.deleteTrial
• PhysiCellModelManager.disassembleIntracellular
• PhysiCellModelManager.domainPath
• PhysiCellModelManager.elementIsTerminal
• PhysiCellModelManager.eraseSimulationIDFromConstituents
• PhysiCellModelManager.evaluateFunctionOnSampling
• PhysiCellModelManager.executableExists
• PhysiCellModelManager.executeStudio
• PhysiCellModelManager.exportIntracellular
• PhysiCellModelManager.exportSimulation
• PhysiCellModelManager.finalPopulationCount
• PhysiCellModelManager.findCentralDB
• PhysiCellModelManager.findComponentID
• PhysiCellModelManager.folderIsVaried
• PhysiCellModelManager.formatTimeRange
• PhysiCellModelManager.fullSavePath
• PhysiCellModelManager.fusionPath
• PhysiCellModelManager.generateLHSCDFs
• PhysiCellModelManager.generateRBDCDFs
• PhysiCellModelManager.generateSobolCDFs
• PhysiCellModelManager.getAllParameterValues
• PhysiCellModelManager.getCellDataSequence
• PhysiCellModelManager.getChildByAttribute
• PhysiCellModelManager.getChildByChildContent
• PhysiCellModelManager.getMeanCounts
• PhysiCellModelManager.getMonadIDDataFrame
• PhysiCellModelManager.getMonadIDs
• PhysiCellModelManager.getParameterValue
• PhysiCellModelManager.getSimpleContent
• PhysiCellModelManager.getSimulationIDs
• PhysiCellModelManager.gitDirectoryIsClean
• PhysiCellModelManager.gitRemotes
• PhysiCellModelManager.graphInfo
• PhysiCellModelManager.icCellParameterName
• PhysiCellModelManager.icCellsPath
• PhysiCellModelManager.icECMParameterName
• PhysiCellModelManager.icECMPath
• PhysiCellModelManager.icFilename
• PhysiCellModelManager.importProject
• PhysiCellModelManager.indexToFilename
• PhysiCellModelManager.inferDeathModelPath
• PhysiCellModelManager.initialParameterDistributionPath
• PhysiCellModelManager.initializeDatabase
• PhysiCellModelManager.initializeModelManager
• PhysiCellModelManager.inputFolderID
• PhysiCellModelManager.inputFolderName
• PhysiCellModelManager.inputIDsSubSchema
• PhysiCellModelManager.inputVariationIDsSubSchema
• PhysiCellModelManager.inputsDict
• PhysiCellModelManager.insertFolder
• PhysiCellModelManager.integrityPath
• PhysiCellModelManager.intracellularAssemblyManifestsEquivalent
• PhysiCellModelManager.intracellularFolder
• PhysiCellModelManager.isCrossPCF
• PhysiCellModelManager.isInitialized
• PhysiCellModelManager.isPhysiECMInConfig
• PhysiCellModelManager.isRoadRunnerInConfig
• PhysiCellModelManager.isRoadRunnerInInputs
• PhysiCellModelManager.isRunningOnHPC
• PhysiCellModelManager.isStarted
• PhysiCellModelManager.latestReleaseTag
• PhysiCellModelManager.libRoadRunnerOnPath
• PhysiCellModelManager.loadCells!
• PhysiCellModelManager.loadCustomCode
• PhysiCellModelManager.loadGraph!
• PhysiCellModelManager.loadMesh!
• PhysiCellModelManager.loadSubstrates!
• PhysiCellModelManager.locationFolder
• PhysiCellModelManager.locationIDName
• PhysiCellModelManager.locationIDNames
• PhysiCellModelManager.locationPath
• PhysiCellModelManager.locationPath
• PhysiCellModelManager.locationPath
• PhysiCellModelManager.locationTableName
• PhysiCellModelManager.locationVariationIDName
• PhysiCellModelManager.locationVariationIDNames
• PhysiCellModelManager.locationVariationsDBName
• PhysiCellModelManager.locationVariationsDatabase
• PhysiCellModelManager.locationVariationsFolder
• PhysiCellModelManager.locationVariationsTable
• PhysiCellModelManager.locationVariationsTable
• PhysiCellModelManager.locationVariationsTable
• PhysiCellModelManager.locationVariationsTable
• PhysiCellModelManager.locationVariationsTable
• PhysiCellModelManager.locationVariationsTableName
• PhysiCellModelManager.lowerClassString
• PhysiCellModelManager.makeMovie
• PhysiCellModelManager.makeXMLPath
• PhysiCellModelManager.makeXMLPath
• PhysiCellModelManager.mechanicsPath
• PhysiCellModelManager.meshInfo
• PhysiCellModelManager.metadataDescription
• PhysiCellModelManager.methodString
• PhysiCellModelManager.monadIDs
• PhysiCellModelManager.monadsSchema
• PhysiCellModelManager.motilityPath
• PhysiCellModelManager.motilityStatistics
• PhysiCellModelManager.necessaryInputsPresent
• PhysiCellModelManager.necrosisPath
• PhysiCellModelManager.orthogonalLHS
• PhysiCellModelManager.parseProjectInputsConfigurationFile
• PhysiCellModelManager.parseValueFromString
• PhysiCellModelManager.pathToInputsConfig
• PhysiCellModelManager.pathToOutputFileBase
• PhysiCellModelManager.pathToOutputFileBase
• PhysiCellModelManager.pathToOutputFolder
• PhysiCellModelManager.pathToOutputXML
• PhysiCellModelManager.pathToOutputXML
• PhysiCellModelManager.pcfConstants
• PhysiCellModelManager.pcfSnapshotCalculation
• PhysiCellModelManager.pcmmDBVersion
• PhysiCellModelManager.pcmmLogo
• PhysiCellModelManager.pcmmVersion
• PhysiCellModelManager.pcmmVersionTableName
• PhysiCellModelManager.perturbVariation
• PhysiCellModelManager.phagocytosisPath
• PhysiCellModelManager.phenotypePath
• PhysiCellModelManager.physiCellCommitHash
• PhysiCellModelManager.physicellDir
• PhysiCellModelManager.physicellEmptyGraph
• PhysiCellModelManager.physicellInfo
• PhysiCellModelManager.physicellIsGit
• PhysiCellModelManager.physicellVersion
• PhysiCellModelManager.physicellVersionsSchema
• PhysiCellModelManager.plotbycelltype
• PhysiCellModelManager.populateTableOnFeatureSubset
• PhysiCellModelManager.populationCount
• PhysiCellModelManager.populationTimeSeries
• PhysiCellModelManager.postVariationXMLProcessing
• PhysiCellModelManager.prepCmdForWrap
• PhysiCellModelManager.prepareBaseFile
• PhysiCellModelManager.prepareBaseRulesetsCollectionFile
• PhysiCellModelManager.prepareHPCCommand
• PhysiCellModelManager.prepareIntracellularImport
• PhysiCellModelManager.prepareLibRoadRunner
• PhysiCellModelManager.preparePCF!
• PhysiCellModelManager.preparePCFPlot
• PhysiCellModelManager.prepareRulesetsCollectionImport
• PhysiCellModelManager.prepareSimulationCommand
• PhysiCellModelManager.prepareVariedInputFolder
• PhysiCellModelManager.prepareVariedInputFolder
• PhysiCellModelManager.printInputFolders
• PhysiCellModelManager.printNewFolders!
• PhysiCellModelManager.printSimulationsTable
• PhysiCellModelManager.printTogether!
• PhysiCellModelManager.printVariationID
• PhysiCellModelManager.processDistance
• PhysiCellModelManager.processExcludeCellTypes
• PhysiCellModelManager.processIncludeCellTypes
• PhysiCellModelManager.processPCFCellTypes
• PhysiCellModelManager.processSimulationTask
• PhysiCellModelManager.processSuccessfulImport
• PhysiCellModelManager.processTime
• PhysiCellModelManager.projectLocations
• PhysiCellModelManager.pruneSimulationOutput
• PhysiCellModelManager.queryToDataFrame
• PhysiCellModelManager.quietRun
• PhysiCellModelManager.readMacrosFile
• PhysiCellModelManager.readPhysiCellGraph!
• PhysiCellModelManager.recognizedStatusCodes
• PhysiCellModelManager.recordConstituentIDs
• PhysiCellModelManager.recordSensitivityScheme
• PhysiCellModelManager.recurseToGetParameterValues!
• PhysiCellModelManager.reinitializeDatabase
• PhysiCellModelManager.repoOwner
• PhysiCellModelManager.requestHeaders
• PhysiCellModelManager.resetDatabase
• PhysiCellModelManager.resetFolder
• PhysiCellModelManager.resolveMovieGlobals
• PhysiCellModelManager.resolvePCMMVersion
• PhysiCellModelManager.resolvePhysiCellVersionID
• PhysiCellModelManager.resolveProjectSource!
• PhysiCellModelManager.resolveProjectSources!
• PhysiCellModelManager.resolveSimulation
• PhysiCellModelManager.resolveStudioGlobals
• PhysiCellModelManager.retrieveElement
• PhysiCellModelManager.retrieveElementError
• PhysiCellModelManager.revertConfig
• PhysiCellModelManager.revertCustomCPP
• PhysiCellModelManager.revertCustomHeader
• PhysiCellModelManager.revertCustomModules
• PhysiCellModelManager.revertMain
• PhysiCellModelManager.revertMakefile
• PhysiCellModelManager.revertSimulationFolderToCurrentPhysiCell
• PhysiCellModelManager.rm_hpc_safe
• PhysiCellModelManager.ruleParameterName
• PhysiCellModelManager.rulePath
• PhysiCellModelManager.rulesetConfig
• PhysiCellModelManager.runAbstractTrial
• PhysiCellModelManager.runSensitivitySampling
• PhysiCellModelManager.runStudio
• PhysiCellModelManager.samplingSimulationIDs
• PhysiCellModelManager.samplingsSchema
• PhysiCellModelManager.sanitizePathElement
• PhysiCellModelManager.secretionPath
• PhysiCellModelManager.sensitivityResults!
• PhysiCellModelManager.setECMSetupElement
• PhysiCellModelManager.setFolderAndFilename!
• PhysiCellModelManager.setJobOptions
• PhysiCellModelManager.setMarchFlag
• PhysiCellModelManager.setNumberOfParallelSims
• PhysiCellModelManager.setSimpleContent
• PhysiCellModelManager.setUpColumns
• PhysiCellModelManager.setUpComponents
• PhysiCellModelManager.setUpICCell
• PhysiCellModelManager.setUpICECM
• PhysiCellModelManager.setUpICFolder
• PhysiCellModelManager.setUpInputs
• PhysiCellModelManager.setUpPhysiCell
• PhysiCellModelManager.setUpRequiredFolders
• PhysiCellModelManager.setUpScripts
• PhysiCellModelManager.setUpStudioInputs
• PhysiCellModelManager.setUpTemplate
• PhysiCellModelManager.shellCommandExists
• PhysiCellModelManager.shortConfigVariationName
• PhysiCellModelManager.shortICCellVariationName
• PhysiCellModelManager.shortICECMVariationName
• PhysiCellModelManager.shortIntracellularVariationName
• PhysiCellModelManager.shortLocationVariationID
• PhysiCellModelManager.shortLocationVariationID
• PhysiCellModelManager.shortRulesetsVariationName
• PhysiCellModelManager.shortVariationName
• PhysiCellModelManager.simulationFailed
• PhysiCellModelManager.simulationIDs
• PhysiCellModelManager.simulationIDs
• PhysiCellModelManager.simulationIDs
• PhysiCellModelManager.simulationRuntimeIntervals
• PhysiCellModelManager.simulationsTable
• PhysiCellModelManager.simulationsTableFromQuery
• PhysiCellModelManager.sqliteDataType
• PhysiCellModelManager.statusCodeID
• PhysiCellModelManager.stmtToDataFrame
• PhysiCellModelManager.substrateNames
• PhysiCellModelManager.substratePath
• PhysiCellModelManager.svgSavePath
• PhysiCellModelManager.tableColumns
• PhysiCellModelManager.tableExists
• PhysiCellModelManager.tableIDName
• PhysiCellModelManager.timePath
• PhysiCellModelManager.transformationPath
• PhysiCellModelManager.trialFolder
• PhysiCellModelManager.trialFolder
• PhysiCellModelManager.trialID
• PhysiCellModelManager.trialID
• PhysiCellModelManager.trialID
• PhysiCellModelManager.trialMonads
• PhysiCellModelManager.trialSimulationIDs
• PhysiCellModelManager.trialType
• PhysiCellModelManager.trialType
• PhysiCellModelManager.updateDatabaseOnCompletion
• PhysiCellModelManager.updateIntracellularComponentIDs!
• PhysiCellModelManager.upgradePCMM
• PhysiCellModelManager.upgradeToVX_Y_Z
• PhysiCellModelManager.useHPC
• PhysiCellModelManager.userParameterPath
• PhysiCellModelManager.userParametersPath
• PhysiCellModelManager.validateParsBytes
• PhysiCellModelManager.variationDataType
• PhysiCellModelManager.variationIDs
• PhysiCellModelManager.variationLocation
• PhysiCellModelManager.variationTarget
• PhysiCellModelManager.variationValue
• PhysiCellModelManager.variationValues
• PhysiCellModelManager.variationValues
• PhysiCellModelManager.variationValues
• PhysiCellModelManager.variationsToMonads
• PhysiCellModelManager.versionFromTable
• PhysiCellModelManager.volumePath
• PhysiCellModelManager.writeDescriptionToMetadata
• PhysiCellModelManager.writePhysiCellCommitHash
• PhysiCellModelManager.DeprecateKeywords.@depkws