def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorA",
"SimpleExample",
self.oscillatorAFileName, "a")
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorB",
"SimpleExample",
self.oscillatorBFileName, "a")
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorA")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorA")
k1 = self.k1_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorB")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorB")
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorA")
GG_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorB")
self.modifyContactEnergies(BB_offset, GG_offset, self.steadyState)
# ############## Write adhesion data to an output file ################
self.writeContactEnergies(mcs, self.contactEnergyOutputFile, "a")
def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorA", "SimpleExample", self.oscillatorAFileName, "a" )
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorB", "SimpleExample", self.oscillatorBFileName, "a" )
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorA" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorA" )
k1 = self.k1_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorB" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorB" )
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorA" )
GG_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorB" )
self.modifyContactEnergies( BB_offset, GG_offset, self.steadyState )
# ############## Write adhesion data to an output file ################
self.writeContactEnergies( mcs, self.contactEnergyOutputFile, "a" )
def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorA",
"SimpleExample",
self.oscillatorAFileName, "a")
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorB",
"SimpleExample",
self.oscillatorBFileName, "a")
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorA")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorA")
k1 = self.k1_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorB")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorB")
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorA")
GG_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorB")
self.modifyContactEnergies(BB_offset, GG_offset, self.steadyState)
# ############## Write adhesion data to an output file ################
self.writeContactEnergies(mcs, self.contactEnergyOutputFile, "a")
if not (mcs % 10):
for cell in self.cellList:
pixelList = self.getCellPixelList(cell)
for pixelTrackerData in pixelList:
self.cellField.set(pixelTrackerData.pixel, None)
break
if mcs > 200:
for cell in self.cellList:
cell.targetVolume = 0.0
cell.lambdaVolume = 200.0
cell.targetSurface = 0.0
cell.lambdaSurface = 200.0
def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorA", "SimpleExample", self.oscillatorAFileName, "a" )
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorB", "SimpleExample", self.oscillatorBFileName, "a" )
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorA" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorA" )
k1 = self.k1_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorB" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorB" )
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorA" )
GG_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorB" )
self.modifyContactEnergies( BB_offset, GG_offset, self.steadyState )
# ############## Write adhesion data to an output file ################
self.writeContactEnergies( mcs, self.contactEnergyOutputFile, "a" )
if not (mcs %10):
for cell in self.cellList:
pixelList=self.getCellPixelList(cell)
for pixelTrackerData in pixelList:
self.cellField.set(pixelTrackerData.pixel,None)
break
if mcs >200:
for cell in self.cellList:
cell.targetVolume=0.0
cell.lambdaVolume=200.0
cell.targetSurface=0.0
cell.lambdaSurface=200.0