def __init__(self, filename=None):
ecell.ecs.setDMSearchPath( os.pathsep.join( ecell.config.dm_path ) )
self.sim = ecell.emc.Simulator()
if ecell.config.version < '3.2.0':
self.ses = Session(self.sim, changeDirectory=False)
else:
self.ses = Session(self.sim)
# Load the model
self.ses.loadModel(filename)
self.molToTrack = ('ca',
'moles_bound_ca_per_moles_cam',
'Rbar',
'PP2Bbar',
'CaMKIIbar',
'PP1abar', # Active PP1/Total PP1
'AMPAR', #
'AMPAR_P',
'D',
'totDp',
'Dpbar'
)
# Tracking the calcium
self.ca = self.ses.createEntityStub( 'Variable:/Spine:ca' )
self.CaMKIIbar = self.ses.createEntityStub( 'Variable:/Spine:CaMKIIbar' )
self.ampar_P = self.ses.createEntityStub('Variable:/Spine:AMPAR_P')
self.ca_in = self.ses.createEntityStub('Process:/Spine:ca_in')
self.ca_leak = self.ses.createEntityStub('Process:/Spine:ca_leak')
self.ca_pump = self.ses.createEntityStub('Process:/Spine:ca_pump')
def __init__(self, filename=None):
ecell.ecs.setDMSearchPath(os.pathsep.join(ecell.config.dm_path))
self.sim = ecell.emc.Simulator()
if ecell.config.version < '3.2.0':
self.ses = Session(self.sim, changeDirectory=False)
else:
self.ses = Session(self.sim)
# Load the model
self.ses.loadModel(filename)
self.molToTrack = (
'ca',
'moles_bound_ca_per_moles_cam',
'Rbar',
'PP2Bbar',
'CaMKIIbar',
'PP1abar', # Active PP1/Total PP1
'AMPAR', #
'AMPAR_P',
'D',
'totDp',
'Dpbar')
# Tracking the calcium
self.ca = self.ses.createEntityStub('Variable:/Spine:ca')
self.CaMKIIbar = self.ses.createEntityStub('Variable:/Spine:CaMKIIbar')
self.ampar_P = self.ses.createEntityStub('Variable:/Spine:AMPAR_P')
self.ca_in = self.ses.createEntityStub('Process:/Spine:ca_in')
self.ca_leak = self.ses.createEntityStub('Process:/Spine:ca_leak')
self.ca_pump = self.ses.createEntityStub('Process:/Spine:ca_pump')
class QuickEcell():
def __init__(self, filename):
"""Initialize Ecell simulator creating a session and a simulator object
and loading the model."""
# set DM library
ecell.ecs.setDMSearchPath( os.pathsep.join( ecell.config.dm_path ) )
# create sim obj
self.sim = ecell.emc.Simulator()
# create the session obj
self.ses = Session(self.sim, changeDirectory=False)
# Lod the model
try:
self.ses.loadModel(filename)
except IOError:
print "IOError: File %s not found." %filename
def create_loggers(self, variables):
"""Create the loggers. The variable name is the Key, the ecell logger obj
is the Value"""
loggers = {}
for var in variables:
try:
loggers[var] = self.ses.createLoggerStub('Variable:/:' + var + ':Value')
loggers[var].create()
except RuntimeError:
print "Variable %s not in the model" %var
print "You need to use the same name you've used in the em file."
return loggers
def run_and_plot(self, time, variables, loggers):
"""Run the simulator and plot all the variables in the variables."""
self.ses.run(time)
for var in variables:
self.plot_var(var, loggers)
plt.legend(loc=0)
def plot_var(self, var, loggers):
"Plot the specific variable"
try:
var_array = loggers[var].getData()
plt.plot(var_array[:,0], var_array[:,1], label=var)
except RuntimeError:
print "Var %s not in the loggers. Skipping" %var
def __init__(self, filename):
"""Initialize Ecell simulator creating a session and a simulator object
and loading the model."""
# set DM library
ecell.ecs.setDMSearchPath( os.pathsep.join( ecell.config.dm_path ) )
# create sim obj
self.sim = ecell.emc.Simulator()
# create the session obj
self.ses = Session(self.sim, changeDirectory=False)
# Lod the model
try:
self.ses.loadModel(filename)
except IOError:
print "IOError: File %s not found." %filename
class EcellManager():
"""Control and instatiate the ecell simulator embedding it in an handy python object"""
def __init__(self, filename=None):
ecell.ecs.setDMSearchPath( os.pathsep.join( ecell.config.dm_path ) )
self.sim = ecell.emc.Simulator()
if ecell.config.version < '3.2.0':
self.ses = Session(self.sim, changeDirectory=False)
else:
self.ses = Session(self.sim)
# Load the model
self.ses.loadModel(filename)
self.molToTrack = ('ca',
'moles_bound_ca_per_moles_cam',
'Rbar',
'PP2Bbar',
'CaMKIIbar',
'PP1abar', # Active PP1/Total PP1
'AMPAR', #
'AMPAR_P',
'D',
'totDp',
'Dpbar'
)
# Tracking the calcium
self.ca = self.ses.createEntityStub( 'Variable:/Spine:ca' )
self.CaMKIIbar = self.ses.createEntityStub( 'Variable:/Spine:CaMKIIbar' )
self.ampar_P = self.ses.createEntityStub('Variable:/Spine:AMPAR_P')
self.ca_in = self.ses.createEntityStub('Process:/Spine:ca_in')
self.ca_leak = self.ses.createEntityStub('Process:/Spine:ca_leak')
self.ca_pump = self.ses.createEntityStub('Process:/Spine:ca_pump')
def createLoggers(self):
"""Create the logger to track the species"""
loggers = {}
#log = ecell.LoggerStub()
for mol in self.molToTrack:
loggers[mol] = self.ses.createLoggerStub( "Variable:/Spine:" + mol
+ ":Value" )
loggers[mol].create() # This creat the Logger Object in the backend
if mol == 'ca':
loggers['ca_conc'] = self.ses.createLoggerStub( "Variable:/Spine:" + mol
+ ":MolarConc" )
loggers['ca_conc'].create() # This creat the Logger Object in the backend
self.loggers = loggers
def calcWeight(CaMKIIbar, PP2Bbar, alpha, beta, n=3, k=0.5):
"""Calc the weight of the synapses according to the CaMKII and Pospahtases
PP2B and PP1"""
# CaMKII term
CaMKII_factor = math.pow(CaMKIIbar, n) / (math.pow(k, n) +
math.pow(CaMKIIbar, n))
Phosphatase_factor = math.pow(PP2Bbar, n) / (math.pow(k, n) +
math.pow(PP2Bbar, n))
scaled_CaMKII_factor = alpha * CaMKII_factor
scaled_Phospatese_factor = beta * Phosphatase_factor
weight = 1 + scaled_CaMKII_factor - scaled_Phospatese_factor
s = "Weight: %s CaMKII factor %s, Phosphatase factor %s" %(weight,
scaled_CaMKII_factor,
scaled_Phospatese_factor)
return weight
def calcium_peak(self, k_value, duration):
"""
Mimic the calcium peak
:Parameters
k_value: the rate of calcium to enter
duration: Duration of the spike
"""
basal = self.ca_in['k']
self.ca_in['k'] = k_value
self.ses.run(duration)
self.ca_in['k'] = basal
def calciumTrain(self, spikes=30, interval=0.1):
"""Create a train of calcium with the specified number of spikes and interval
:Parameter
spikes: number of spikes
interval: Interval between spikes
"""
for i in range(spikes):
self.calcium_peak(4.0e8, # Magic number from Lu
0.00001 #Really fast spike to avoid the overlap
)
self.ses.run(interval)
def converToTimeCourses(self):
timeCourses = {}
for key in self.loggers:
timeCourses[key] = self.loggers[key].getData()
self.timeCourses = timeCourses
class EcellManager():
"""Control and instatiate the ecell simulator embedding it in an handy python object"""
def __init__(self, filename=None):
ecell.ecs.setDMSearchPath(os.pathsep.join(ecell.config.dm_path))
self.sim = ecell.emc.Simulator()
if ecell.config.version < '3.2.0':
self.ses = Session(self.sim, changeDirectory=False)
else:
self.ses = Session(self.sim)
# Load the model
self.ses.loadModel(filename)
self.molToTrack = (
'ca',
'moles_bound_ca_per_moles_cam',
'Rbar',
'PP2Bbar',
'CaMKIIbar',
'PP1abar', # Active PP1/Total PP1
'AMPAR', #
'AMPAR_P',
'D',
'totDp',
'Dpbar')
# Tracking the calcium
self.ca = self.ses.createEntityStub('Variable:/Spine:ca')
self.CaMKIIbar = self.ses.createEntityStub('Variable:/Spine:CaMKIIbar')
self.ampar_P = self.ses.createEntityStub('Variable:/Spine:AMPAR_P')
self.ca_in = self.ses.createEntityStub('Process:/Spine:ca_in')
self.ca_leak = self.ses.createEntityStub('Process:/Spine:ca_leak')
self.ca_pump = self.ses.createEntityStub('Process:/Spine:ca_pump')
def createLoggers(self):
"""Create the logger to track the species"""
loggers = {}
#log = ecell.LoggerStub()
for mol in self.molToTrack:
loggers[mol] = self.ses.createLoggerStub("Variable:/Spine:" + mol +
":Value")
loggers[mol].create(
) # This creat the Logger Object in the backend
if mol == 'ca':
loggers['ca_conc'] = self.ses.createLoggerStub(
"Variable:/Spine:" + mol + ":MolarConc")
loggers['ca_conc'].create(
) # This creat the Logger Object in the backend
self.loggers = loggers
def calcWeight(CaMKIIbar, PP2Bbar, alpha, beta, n=3, k=0.5):
"""Calc the weight of the synapses according to the CaMKII and Pospahtases
PP2B and PP1"""
# CaMKII term
CaMKII_factor = math.pow(CaMKIIbar,
n) / (math.pow(k, n) + math.pow(CaMKIIbar, n))
Phosphatase_factor = math.pow(
PP2Bbar, n) / (math.pow(k, n) + math.pow(PP2Bbar, n))
scaled_CaMKII_factor = alpha * CaMKII_factor
scaled_Phospatese_factor = beta * Phosphatase_factor
weight = 1 + scaled_CaMKII_factor - scaled_Phospatese_factor
s = "Weight: %s CaMKII factor %s, Phosphatase factor %s" % (
weight, scaled_CaMKII_factor, scaled_Phospatese_factor)
return weight
def calcium_peak(self, k_value, duration):
"""
Mimic the calcium peak
:Parameters
k_value: the rate of calcium to enter
duration: Duration of the spike
"""
basal = self.ca_in['k']
self.ca_in['k'] = k_value
self.ses.run(duration)
self.ca_in['k'] = basal
def calciumTrain(self, spikes=30, interval=0.1):
"""Create a train of calcium with the specified number of spikes and interval
:Parameter
spikes: number of spikes
interval: Interval between spikes
"""
for i in range(spikes):
self.calcium_peak(
4.0e8, # Magic number from Lu
0.00001 #Really fast spike to avoid the overlap
)
self.ses.run(interval)
def converToTimeCourses(self):
timeCourses = {}
for key in self.loggers:
timeCourses[key] = self.loggers[key].getData()
self.timeCourses = timeCourses