def writeXMLDescriptionFile(self,_fileName=""):
from os.path import join
"""
This function will write XML description of the stored fields. It has to be called after
initialization of theCMLFieldHandler is completed
"""
import CompuCellSetup
latticeTypeStr = CompuCellSetup.ExtractLatticeType()
if latticeTypeStr=="":
latticeTypeStr = "Square"
typeIdTypeNameDict = CompuCellSetup.ExtractTypeNamesAndIds()
print "typeIdTypeNameDict",typeIdTypeNameDict
from XMLUtils import ElementCC3D
dim = self.sim.getPotts().getCellFieldG().getDim()
numberOfSteps = self.sim.getNumSteps()
latticeDataXMLElement=ElementCC3D("CompuCell3DLatticeData",{"Version":"1.0"})
latticeDataXMLElement.ElementCC3D("Dimensions",{"x":str(dim.x),"y":str(dim.y),"z":str(dim.z)})
latticeDataXMLElement.ElementCC3D("Lattice",{"Type":latticeTypeStr})
latticeDataXMLElement.ElementCC3D("Output",{"Frequency":str(self.outputFrequency),"NumberOfSteps":str(numberOfSteps),"CoreFileName":self.outputFileCoreName,"Directory":self.outputDirName})
#output information about cell type names and cell ids. It is necessary during generation of the PIF files from VTK output
for typeId in typeIdTypeNameDict.keys():
latticeDataXMLElement.ElementCC3D("CellType",{"TypeName":str(typeIdTypeNameDict[typeId]),"TypeId":str(typeId)})
fieldsXMLElement=latticeDataXMLElement.ElementCC3D("Fields")
for fieldName in self.fieldTypes.keys():
fieldsXMLElement.ElementCC3D("Field",{"Name":fieldName,"Type":self.fieldTypes[fieldName]})
# writing XML description to the disk
if _fileName!="":
latticeDataXMLElement.CC3DXMLElement.saveXML(str(_fileName))
else:
latticeDataFileName = join(self.outputDirName,self.outputFileCoreName+"LDF.dml")
latticeDataXMLElement.CC3DXMLElement.saveXML(str(latticeDataFileName))
def start(self):
# #################### Create SBML models ######################
sbmlModelName = "DeltaNotchModel"
sbmlModelKey = "DN"
sbmlModelPath = "Simulation/MinimalDeltaNotch.sbml"
timeStepOfIntegration = 0.1
bionetAPI.loadSBMLModel(sbmlModelName, sbmlModelPath, sbmlModelKey,
timeStepOfIntegration)
# ################ Add SBML models to cell types ##################
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "LowDelta")
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "HighDelta")
## Include this for a test
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "External")
# ####### Set initial conditions for SBML properties #########
bionetAPI.setBionetworkInitialCondition("LowDelta", "DN_di", 0.2)
bionetAPI.setBionetworkInitialCondition("HighDelta", "DN_di", 0.8)
for cell in self.cellList:
cell.targetVolume = 32.0
cell.lambdaVolume = 1.0
cell.targetSurface = 32.0
cell.lambdaSurface = 1.0
# ######## Create bionetworks and initialize their states ##########
bionetAPI.initializeBionetworks()
# ######## Set cell initial conditions by individual cell ##########
for cell in self.cellList:
dictionaryAttrib = CompuCell.getPyAttrib(cell)
dictionaryAttrib["InitialVolume"] = cell.volume
dictionaryAttrib["DivideVolume"] = 2. * cell.volume
self.initialNumberOfCells = len(self.cellList)
print "\n\nNumber of cells: %s\n\n" % self.initialNumberOfCells
import CompuCellSetup
self.cellTypeMap = CompuCellSetup.ExtractTypeNamesAndIds()
del (self.cellTypeMap[0])
def start(self):
# #################### Load SBML models ######################
## Create a bionetwork SBML model named "DeltaNotchModel"
sbmlModelName = "DeltaNotchModel"
sbmlModelKey = "DN"
sbmlModelPath = "Simulation/MinimalDeltaNotch.sbml"
timeStepOfIntegration = 0.1
bionetAPI.loadSBMLModel(sbmlModelName, sbmlModelPath, sbmlModelKey,
timeStepOfIntegration)
# ################ Add SBML models to celltype-specific bionetwork template libraries ##################
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "LowDelta")
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "HighDelta")
## Include this for a test
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "External")
# ####### Set initial conditions for SBML properties #########
bionetAPI.setBionetworkInitialCondition("LowDelta", "DN_di", 0.2)
bionetAPI.setBionetworkInitialCondition("HighDelta", "DN_di", 0.8)
# ######## Create bionetworks and initialize their states ##########
bionetAPI.initializeBionetworks()
# ######## Set cell initial conditions by individual cell ##########
for cell in self.cellList:
cell.dict["InitialVolume"] = cell.volume
cell.dict["DivideVolume"] = 2. * cell.volume
cell.targetVolume = 32.0
cell.lambdaVolume = 1.0
import CompuCellSetup
self.cellTypeMap = CompuCellSetup.ExtractTypeNamesAndIds()
del (self.cellTypeMap[0])
def start(self):
# #################### Create SBML models ######################
## Create a bionetwork SBML model named "DeltaNotchModel"
sbmlModelName = "DeltaNotchModel"
sbmlModelKey = "DN"
sbmlModelPath = "Simulation/MinimalDeltaNotch.sbml"
timeStepOfIntegration = 0.05
bionetAPI.loadSBMLModel(sbmlModelName, sbmlModelPath, sbmlModelKey,
timeStepOfIntegration)
## Create a bionetwork SBML model named "CadherinCatenin"
sbmlModelPath = "Simulation/CadherinCatenin_RamisConde2008.sbml"
bionetAPI.loadSBMLModel("CadherinCatenin", sbmlModelPath, "CC", 0.05)
## Create a bionetwork SBML model named "BloodLiverPK"
sbmlModelPath = "Simulation/PK_BloodLiver.sbml"
bionetAPI.loadSBMLModel("BloodLiverPK", sbmlModelPath, "BLPK", 0.05)
## Create a bionetwork SBML model named "SimpleExample"
sbmlModelPath = "Simulation/SimpleExample.sbml"
bionetAPI.loadSBMLModel("SimpleExample", sbmlModelPath, "SE", 0.05)
# ################ Add SBML models to bionetwork template libraries ##################
## Add SBML model to CellTypeA
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "CellTypeA")
bionetAPI.addSBMLModelToTemplateLibrary("BloodLiverPK", "CellTypeA")
## Add SBML models to CellTypeB
bionetAPI.addSBMLModelToTemplateLibrary("DeltaNotchModel", "CellTypeB")
bionetAPI.addSBMLModelToTemplateLibrary("CadherinCatenin", "CellTypeB")
## Add SBML models to CellTypeC
bionetAPI.addSBMLModelToTemplateLibrary("CadherinCatenin", "CellTypeC")
## Add SBML models to CellTypeD
bionetAPI.addSBMLModelToTemplateLibrary("BloodLiverPK", "CellTypeD")
bionetAPI.addSBMLModelToTemplateLibrary("SimpleExample", "CellTypeD")
# ####### Set initial conditions for SBML properties #########
## Set global (for all bionetwork template libraries) SBML initial conditions
bionetAPI.setBionetworkInitialCondition("Global", "DN_di", 0.4)
bionetAPI.setBionetworkInitialCondition("Global", "CC_beta", 24)
bionetAPI.setBionetworkInitialCondition("Global", "Ab", 1.1)
## Set SBML initial conditions for CellTypeA
bionetAPI.setBionetworkInitialCondition("CellTypeA", "DN_ni", 0.8)
## Set SBML initial conditions for CellTypeB
bionetAPI.setBionetworkInitialCondition("CellTypeB", "CC_Ebeta",
33.333)
bionetAPI.setBionetworkInitialCondition("CellTypeB", "BLPK_A1",
0.44444)
## Set SBML initial conditions for CellTypeC
bionetAPI.setBionetworkInitialCondition("CellTypeC", "CC_Ebeta",
4.32111)
bionetAPI.setBionetworkInitialCondition("CellTypeC", "SE_S1",
0.66666666)
bionetAPI.setBionetworkInitialCondition("CellTypeC", "CLK_Nan1",
0.55555)
## Set SBML initial conditions for CellTypeD
bionetAPI.setBionetworkInitialCondition("CellTypeD", "CC_Emem",
12.34567)
bionetAPI.setBionetworkInitialCondition("CellTypeD", "CLK_Nan1",
0.77777)
bionetAPI.setBionetworkInitialCondition("CellTypeD", "DN_ni",
0.88888888)
## Setting SBML initial conditions for non-existent cell type
bionetAPI.setBionetworkInitialCondition("NonExistentCellType", "SE_S1",
0.62)
# ######## Create bionetworks and initialize their states ##########
bionetAPI.initializeBionetworks()
for cell in self.cellList:
cell.dict["InitialVolume"] = cell.volume
cell.dict["DivideVolume"] = 280.
cell.targetVolume = 100.0
cell.lambdaVolume = 2.0
import CompuCellSetup
self.cellTypeMap = CompuCellSetup.ExtractTypeNamesAndIds()
del (self.cellTypeMap[0])
