def loadModel(self):
G.createProject(name = 'Simple Cell')
print('Loading Model...')
self.soma = h.Section(name='soma')
self.dend = h.Section(name='dend')
self.dend.connect(self.soma(1))
# Surface area of cylinder is 2*pi*r*h (sealed ends are implicit).
self.soma.L = self.soma.diam = 12.6157 # Makes a soma of 500 microns squared.
self.dend.L = 200 # microns
self.dend.diam = 1 # microns
for sec in h.allsec():
sec.Ra = 100 # Axial resistance in Ohm * cm
sec.cm = 1 # Membrane capacitance in micro Farads / cm^2
# Insert active Hodgkin-Huxley current in the soma
self.soma.insert('hh')
self.soma.gnabar_hh = 0.12 # Sodium conductance in S/cm2
self.soma.gkbar_hh = 0.036 # Potassium conductance in S/cm2
self.soma.gl_hh = 0.0003 # Leak conductance in S/cm2
self.soma.el_hh = -54.3 # Reversal potential in mV
# Insert passive current in the dendrite
self.dend.insert('pas')
self.dend.g_pas = 0.001 # Passive conductance in S/cm2
self.dend.e_pas = -65 # Leak reversal potential mV
self.dend.nseg = 10
# add synapse (custom channel)
self.syn = h.AlphaSynapse(self.dend(1.0))
self.syn.e = 0 # equilibrium potential in mV
self.syn.onset = 20 # turn on after this time in ms
self.syn.gmax = 0.05 # set conductance in uS
self.syn.tau = 0.1 # set time constant
# record soma voltage and time
self.t_vec = h.Vector()
self.t_vec.record(h._ref_t)
G.createStateVariable(id = 'time', name = 'time', units = 'ms', neuron_variable = self.t_vec)
self.v_vec_soma = h.Vector()
self.v_vec_soma.record(self.soma(1.0)._ref_v) # change recoding pos
#TODO How do we extract the units?
G.createStateVariable(id = 'v_vec_soma', name = 'v_vec_soma', units = 'mV', neuron_variable = self.v_vec_soma)
self.v_vec_dend = h.Vector()
self.v_vec_dend.record(self.dend(1.0)._ref_v)
#TODO How do we extract the units?
G.createStateVariable(id = 'v_vec_dend', name = 'v_vec_dend', units = 'mV', neuron_variable = self.v_vec_dend)
# run simulation
h.tstop = 60 # ms
def loadModel(self):
G.createProject(name='Very Simple Cell')
print('Loading Model...')
self.soma = h.Section(name='soma')
self.soma.insert('pas')
self.asyn = h.AlphaSynapse(self.soma(0.5))
self.asyn.onset = 20
self.asyn.gmax = 1
self.v_vec = h.Vector() # Membrane potential vector
self.t_vec = h.Vector() # Time stamp vector
self.v_vec.record(self.soma(0.5)._ref_v)
G.createStateVariable(id='v_vec',
name='v_vec',
units='mV',
neuron_variable=self.v_vec)
self.t_vec.record(h._ref_t)
G.createStateVariable(id='time',
name='time',
units='ms',
neuron_variable=self.t_vec)
h.tstop = 80.0
def __init__(self, numcells):
G.createProject(name = 'Simple Network')
self.spkt = h.Vector() # Spike time of all cells
self.spkid = h.Vector() # cell ids of spike times
self.create_cells(numcells) # call method to create cells