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 step(self,mcs):
for cell in self.cellList:
if (cell):
D=0.0; nn=0
cellNeighborList=self.getCellNeighbors(cell)
for neighbor in cellNeighborList:
if (neighbor.neighborAddress):
nn+=1
state=bionetAPI.getBionetworkState(neighbor.neighborAddress.id,'DeltaNotch')
D+=state['D']
if (nn>0):
D=D/nn
state={}
state['Davg']=D
bionetAPI.setBionetworkState(cell.id,'DeltaNotch',state)
state=bionetAPI.getBionetworkState(cell.id,'DeltaNotch')
cell.dict['D']=D
cell.dict['N']=state['N']
bionetAPI.timestepBionetworks()