def start(self):
# iterating over all cells in simulation
for cell in self.cellList:
# you can access/manipulate cell properties here
cell.targetVolume=25
cell.lambdaVolume=2.0
#bionet section
modelName = "OSCLI"
modelNickname = "OSC" # this is usually shorter version version of model name
fileDir=os.path.dirname (os.path.abspath( __file__ ))
modelPath=os.path.join(fileDir,"oscli.sbml")
print "Path=",modelPath
integrationStep = 0.02
bionetAPI.loadSBMLModel(modelName , modelPath, modelNickname, integrationStep)
bionetAPI.addSBMLModelToTemplateLibrary("OSCLI","NonCondensing")
bionetAPI.initializeBionetworks()
# iterating over all cells in simulation
state={}
for cell in self.cellList:
if cell.type==self.NONCONDENSING:
state['S1']=0.0
state['S2']=1.0
bionetAPI.setBionetworkState(cell.id,'OSCLI',state)
def start(self):
# iterating over all cells in simulation
for cell in self.cellList:
# you can access/manipulate cell properties here
cell.targetVolume = 25
cell.lambdaVolume = 2.0
#bionet section
modelName = "OSCLI"
modelNickname = "OSC" # this is usually shorter version version of model name
fileDir = os.path.dirname(os.path.abspath(__file__))
modelPath = os.path.join(fileDir, "oscli.sbml")
print "Path=", modelPath
integrationStep = 0.02
bionetAPI.loadSBMLModel(modelName, modelPath, modelNickname,
integrationStep)
bionetAPI.addSBMLModelToTemplateLibrary("OSCLI", "NonCondensing")
bionetAPI.initializeBionetworks()
# iterating over all cells in simulation
state = {}
for cell in self.cellList:
if cell.type == self.NONCONDENSING:
state['S1'] = 0.0
state['S2'] = 1.0
bionetAPI.setBionetworkState(cell.id, 'OSCLI', state)
def start(self):
#Loading model
Name = 'DeltaNotch'
Key = 'DN'
simulationDir=os.path.dirname (os.path.abspath( __file__ ))
Path= os.path.join(simulationDir,'DN_Collier.sbml')
Path=os.path.abspath(Path) # normalizing path
IntegrationStep = 0.2
bionetAPI.loadSBMLModel(Name, Path, Key, IntegrationStep)
bionetAPI.addSBMLModelToTemplateLibrary(Name,'TypeA')
bionetAPI.initializeBionetworks()
#Initial conditions
import random
state={} #dictionary to store state veriables of the SBML model
for cell in self.cellList:
if (cell):
state['D'] = random.uniform(0.9,1.0)
state['N'] = random.uniform(0.9,1.0)
bionetAPI.setBionetworkState(cell.id,'DeltaNotch',state)
cell.dict['D']=state['D']
cell.dict['N']=state['N']
def start(self):
# #################### Create SBML models ######################
## Load a Bionetwork SBML model named "SimpleExample"
sbmlModelPath = "Simulation/SimpleExample.sbml"
bionetAPI.loadSBMLModel( "SimpleExample", sbmlModelPath, "SE", 0.5 )
# ################ Add SBML models to Bionetwork Template Libraries ##################
## Add SBML model to non-cell bionetwork template libaries called "ExternalOscillatorA" and "ExternalOscillatorB"
bionetAPI.addSBMLModelToTemplateLibrary( "SimpleExample", "ExternalOscillatorA" )
bionetAPI.addSBMLModelToTemplateLibrary( "SimpleExample", "ExternalOscillatorB" )
# ####### Set initial conditions for Bionetwork properties #########
## Set initial conditions for "ExternalOscillatorA" and "ExternalOscillatorB" bionetwork template libraries
self.k1_init = 0.1; self.k2_init = 0.1; self.mcsPeriod = 500
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorA", "SE_k1", self.k1_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorA", "SE_k2", self.k2_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorA", "SE_X0", 10.0 )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorB", "SE_k1", self.k1_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorB", "SE_k2", self.k2_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorB", "SE_X0", 10.0 )
# ######## Create Bionetworks (integrators) and initialize their states ##########
bionetAPI.initializeBionetworks()
# ######## Perform initialization tasks and calculations ##########
k1 = bionetAPI.getBionetworkValue( "SE_k1", "ExternalOscillatorA" )
k2 = bionetAPI.getBionetworkValue( "SE_k2", "ExternalOscillatorA" )
X0 = bionetAPI.getBionetworkValue( "SE_X0", "ExternalOscillatorA" )
print "k1=",k1," k2=",k2," X0=",X0
self.steadyState = k1 * X0 / k2
# #### Write bionetwork state variable names of external oscillators to output file
self.oscillatorAFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateA.txt"
bionetAPI.writeBionetworkStateVarNamesToFile( "ExternalOscillatorA", "SimpleExample", self.oscillatorAFileName, "w" )
self.oscillatorBFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateB.txt"
bionetAPI.writeBionetworkStateVarNamesToFile( "ExternalOscillatorB", "SimpleExample", self.oscillatorBFileName, "w" )
# ############## Write adhesion data to an output file ################
self.contactEnergyOutputFile = "Demos/BionetSolverExamples/OscillatingContactEnergies/contactEnergies.txt"
self.writeContactEnergies( 0, self.contactEnergyOutputFile, "w" )
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):
# #################### 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):
# #################### 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 ######################
## Load a Bionetwork SBML model named "SimpleExample"
sbmlModelPath = "Simulation/SimpleExample.sbml"
bionetAPI.loadSBMLModel("SimpleExample", sbmlModelPath, "SE", 0.5)
# ################ Add SBML models to Bionetwork Template Libraries ##################
## Add SBML model to non-cell bionetwork template libaries called "ExternalOscillatorA" and "ExternalOscillatorB"
bionetAPI.addSBMLModelToTemplateLibrary("SimpleExample",
"ExternalOscillatorA")
bionetAPI.addSBMLModelToTemplateLibrary("SimpleExample",
"ExternalOscillatorB")
# ####### Set initial conditions for Bionetwork properties #########
## Set initial conditions for "ExternalOscillatorA" and "ExternalOscillatorB" bionetwork template libraries
self.k1_init = 0.1
self.k2_init = 0.1
self.mcsPeriod = 500
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorA", "SE_k1",
self.k1_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorA", "SE_k2",
self.k2_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorA", "SE_X0",
10.0)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorB", "SE_k1",
self.k1_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorB", "SE_k2",
self.k2_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorB", "SE_X0",
10.0)
# ######## Create Bionetworks (integrators) and initialize their states ##########
bionetAPI.initializeBionetworks()
# ######## Perform initialization tasks and calculations ##########
k1 = bionetAPI.getBionetworkValue("SE_k1", "ExternalOscillatorA")
k2 = bionetAPI.getBionetworkValue("SE_k2", "ExternalOscillatorA")
X0 = bionetAPI.getBionetworkValue("SE_X0", "ExternalOscillatorA")
print "k1=", k1, " k2=", k2, " X0=", X0
self.steadyState = k1 * X0 / k2
# #### Write bionetwork state variable names of external oscillators to output file
self.oscillatorAFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateA.txt"
bionetAPI.writeBionetworkStateVarNamesToFile("ExternalOscillatorA",
"SimpleExample",
self.oscillatorAFileName,
"w")
self.oscillatorBFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateB.txt"
bionetAPI.writeBionetworkStateVarNamesToFile("ExternalOscillatorB",
"SimpleExample",
self.oscillatorBFileName,
"w")
# ############## Write adhesion data to an output file ################
self.contactEnergyOutputFile = "Demos/BionetSolverExamples/OscillatingContactEnergies/contactEnergies.txt"
self.writeContactEnergies(0, self.contactEnergyOutputFile, "w")
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:
dictionaryAttrib = CompuCell.getPyAttrib( cell )
dictionaryAttrib["InitialVolume"] = cell.volume
dictionaryAttrib["DivideVolume"] = 280.
cell.targetVolume = 100.0
cell.lambdaVolume = 2.0
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])