def test_twocomp(sim):
"""Pass a simulation object as parameter"""
spine_area_mult = 2.0
cell = moose.Cell('mycell', sim.model)
soma = MyCompartment('soma', cell)
soma.length = 20e-6
soma.diameter = 2 * 7.5e-6
soma.Em = -65e-3
soma.initVm = -65e-3
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(2.5)
dend = MyCompartment('dend', cell)
dend.length = 40e-6
dend.diameter = 2 * 1.06e-6
dend.Em = -65e-3
dend.initVm = -65e-3
dend.setSpecificCm(9e-3 * spine_area_mult)
dend.setSpecificRm(5.0 / spine_area_mult)
dend.setSpecificRa(2.5)
soma.traubConnect(dend)
vm_table = dend.insertRecorder("Vm1", "Vm", sim.data)
dend.insertPulseGen("pulsegen1", sim.model, firstLevel=3e-10, firstDelay=20e-3, firstWidth=100e-3)
# sim.schedule()
# sim.run(100e-3)
# sim.dump_data("data")
return cell
channel = class_obj(channel_class, lib)
channel.X = 0.0
channel_lib[channel_class] = channel
channels_inited = True
return channel_lib
if __name__ == '__main__':
sim = Simulation('test_ss_soma')
soma = MyCompartment('soma', sim.model)
soma.length = 20e-6
soma.diameter = 2e-6 * 7.5
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(1.0)
soma.Em = -65e-3
soma.initVm = -65e-3
channel_lib = init_channels()
gk = {}
for channel, density in channel_density.items():
chan = channel_lib[channel]
new_chan = moose.HHChannel(chan, chan.name, soma)
chan = soma.insertChannel(new_chan, density)
chan.X = 0.0
gk[channel] = moose.Table(channel, sim.data)
gk[channel].stepMode = 3
gk[channel].connect('inputRequest', chan, 'Gk')
print chan.name, chan.Gbar
if channel.startswith('K'):
chan.Ek = EK
elif channel.startswith('Na'):
from subprocess import call
call(['/home/subha/neuron/nrn/x86_64/bin/nrngui', 'test_suppyrRS_1comp.hoc'], cwd='../nrn')
from datetime import datetime
import moose
import config
from cell import *
from capool import CaPool
from compartment import MyCompartment
from simulation import Simulation
sim = Simulation()
cell = moose.Cell('cell', sim.model)
soma = MyCompartment('soma', cell)
soma.diameter = 16e-6
soma.length = 15e-6
soma.Em = -70e-3
soma.initVm = -65e-3
soma.setSpecificRm(5.0)
soma.setSpecificRa(2.5)
soma.setSpecificCm(9e-3)
soma.insertChannel('NaF', specificGbar=1875.0, Ek=50e-3, shift=-3.5e-3)
soma.insertChannel('CaL', specificGbar=10.0, Ek=125e-3)
soma.insertCaPool(2600000.0, 100e-3)
vmTable = soma.insertRecorder('Vm', 'Vm', sim.data)
caTable = moose.Table('ca', sim.data)
caTable.stepMode = 3
soma.ca_pool.connect('Ca', caTable, 'inputRequest')
sim.schedule()
sim.run(200e-3)
sim.dump_data('data')
else:
channel = class_obj(channel_class, lib)
channel.X = 0.0
channel_lib[channel_class] = channel
channels_inited = True
return channel_lib
if __name__ == '__main__':
sim = Simulation('test_ss_soma')
soma = MyCompartment('soma', sim.model)
soma.length = 20e-6
soma.diameter = 2e-6 * 7.5
soma.setSpecificCm(9e-3)
soma.setSpecificRm(5.0)
soma.setSpecificRa(1.0)
soma.Em = -65e-3
soma.initVm = -65e-3
channel_lib = init_channels()
gk = {}
for channel, density in channel_density.items():
chan = channel_lib[channel]
new_chan = moose.HHChannel(chan, chan.name, soma)
chan = soma.insertChannel(new_chan, density)
chan.X = 0.0
gk[channel] = moose.Table(channel, sim.data)
gk[channel].stepMode = 3
gk[channel].connect('inputRequest', chan, 'Gk')
print chan.name, chan.Gbar
if channel.startswith('K'):
chan.Ek = EK
elif channel.startswith('Na'):