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 )