def step(self, mcs): # ######### Update all bionetwork integrator(s) ########### bionetAPI.timestepBionetworks() bionetAPI.printBionetworkState(1) # ######## Implement cell growth by increasing target volume ########## for cell in self.cellList: dictionaryAttrib = CompuCell.getPyAttrib( cell ) cell.targetVolume = cell.volume + 0.1*dictionaryAttrib["InitialVolume"] # ###### Retrieve delta values and set cell bionetwork template libraries according to delta concentration ######## for cell in self.cellList: currentDelta = bionetAPI.getBionetworkValue( "DN_di", cell.id ) if( currentDelta > 0.5 ): if self.cellTypeMap[cell.type] == "LowDelta": bionetAPI.setBionetworkValue( "TemplateLibrary", "HighDelta", cell.id ) else: if self.cellTypeMap[cell.type] == "HighDelta": bionetAPI.setBionetworkValue( "TemplateLibrary", "LowDelta", cell.id ) # ####### Set all cell dbari values as a function of neighbor delta values ######### for cell in self.cellList: weightedSumOfNeighborDeltaValues = 0.0 neighborContactAreas = bionetAPI.getNeighborContactAreas( cell.id ) neighborDeltaValues = bionetAPI.getNeighborProperty( "DN_di", cell.id ) for neighborID in neighborContactAreas.keys(): weightedSumOfNeighborDeltaValues += (neighborContactAreas[neighborID] * neighborDeltaValues[neighborID]) bionetAPI.setBionetworkValue( "DN_dbari", weightedSumOfNeighborDeltaValues/cell.surface, cell.id )
def step(self, mcs): # ######### Update bionetwork integrator(s) for all cells ########### bionetAPI.timestepBionetworks() # ######## Implement cell growth by increasing target volume ########## for cell in self.cellList: if cell.id > self.initialNumberOfCells: ## All new cells are assigned a target volume of 0 to force cell death cell.targetVolume = 0. cell.lambdaVolume = 2. cell.targetSurface = 0. cell.lambdaSurface = 2. else: dictionaryAttrib = CompuCell.getPyAttrib(cell) cell.targetVolume = cell.volume + 0.15 * dictionaryAttrib[ "InitialVolume"] # ###### Retrieve delta values and set cell type according to delta concentration ######## for cell in self.cellList: currentDeltaValue = bionetAPI.getBionetworkValue("DN_di", cell.id) if (currentDeltaValue > 0.5): if (self.cellTypeMap[cell.type] == "LowDelta"): print "ID of cell to undergo type change %s" % cell.id print "Type of cell to undergo type change %s" % bionetAPI.getBionetworkValue( "TemplateLibrary", cell.id) bionetAPI.setBionetworkValue("TemplateLibrary", "HighDelta", cell.id) else: if (self.cellTypeMap[cell.type] == "HighDelta"): bionetAPI.setBionetworkValue("TemplateLibrary", "LowDelta", cell.id) # ####### Set all cell dbari values as a function of neighbor delta values ######### for cell in self.cellList: weightedSumOfNeighborDeltaValues = 0.0 neighborContactAreas = bionetAPI.getNeighborContactAreas(cell.id) neighborDeltaValues = bionetAPI.getNeighborProperty( "DN_di", cell.id) for neighborID in neighborContactAreas.keys(): weightedSumOfNeighborDeltaValues += ( neighborContactAreas[neighborID] * neighborDeltaValues[neighborID]) bionetAPI.setBionetworkValue( "DN_dbari", weightedSumOfNeighborDeltaValues / cell.surface, cell.id)
def step(self, mcs): # ######### Update all bionetwork integrator(s) ########### bionetAPI.timestepBionetworks() bionetAPI.printBionetworkState(1) # ######## Implement cell growth by increasing target volume ########## for cell in self.cellList: dictionaryAttrib = CompuCell.getPyAttrib(cell) cell.targetVolume = cell.volume + 0.1 * dictionaryAttrib[ "InitialVolume"] # ###### Retrieve delta values and set cell bionetwork template libraries according to delta concentration ######## for cell in self.cellList: currentDelta = bionetAPI.getBionetworkValue("DN_di", cell.id) if (currentDelta > 0.5): if self.cellTypeMap[cell.type] == "LowDelta": bionetAPI.setBionetworkValue("TemplateLibrary", "HighDelta", cell.id) else: if self.cellTypeMap[cell.type] == "HighDelta": bionetAPI.setBionetworkValue("TemplateLibrary", "LowDelta", cell.id) # ####### Set all cell dbari values as a function of neighbor delta values ######### for cell in self.cellList: weightedSumOfNeighborDeltaValues = 0.0 neighborContactAreas = bionetAPI.getNeighborContactAreas(cell.id) neighborDeltaValues = bionetAPI.getNeighborProperty( "DN_di", cell.id) for neighborID in neighborContactAreas.keys(): weightedSumOfNeighborDeltaValues += ( neighborContactAreas[neighborID] * neighborDeltaValues[neighborID]) bionetAPI.setBionetworkValue( "DN_dbari", weightedSumOfNeighborDeltaValues / cell.surface, cell.id)
def step(self, mcs): # ######### Update bionetwork integrator(s) for all cells ########### bionetAPI.timestepBionetworks() # ######## Implement cell growth by increasing target volume ########## for cell in self.cellList: if cell.id > self.initialNumberOfCells: ## All new cells are assigned a target volume of 0 to force cell death cell.targetVolume = 0. cell.lambdaVolume = 2. cell.targetSurface = 0. cell.lambdaSurface = 2. else: dictionaryAttrib = CompuCell.getPyAttrib( cell ) cell.targetVolume = cell.volume + 0.15*dictionaryAttrib["InitialVolume"] # ###### Retrieve delta values and set cell type according to delta concentration ######## for cell in self.cellList: currentDeltaValue = bionetAPI.getBionetworkValue( "DN_di", cell.id ) if( currentDeltaValue > 0.5 ): if( self.cellTypeMap[cell.type] == "LowDelta" ): print "ID of cell to undergo type change %s" % cell.id print "Type of cell to undergo type change %s" % bionetAPI.getBionetworkValue( "TemplateLibrary", cell.id ) bionetAPI.setBionetworkValue( "TemplateLibrary", "HighDelta", cell.id ) else: if( self.cellTypeMap[cell.type] == "HighDelta" ): bionetAPI.setBionetworkValue( "TemplateLibrary", "LowDelta", cell.id ) # ####### Set all cell dbari values as a function of neighbor delta values ######### for cell in self.cellList: weightedSumOfNeighborDeltaValues = 0.0 neighborContactAreas = bionetAPI.getNeighborContactAreas( cell.id ) neighborDeltaValues = bionetAPI.getNeighborProperty( "DN_di", cell.id ) for neighborID in neighborContactAreas.keys(): weightedSumOfNeighborDeltaValues += (neighborContactAreas[neighborID] * neighborDeltaValues[neighborID]) bionetAPI.setBionetworkValue( "DN_dbari", weightedSumOfNeighborDeltaValues/cell.surface, cell.id )