pulse_amp = 1e-9
pulse_delay2 = 1e9
cond_set = {
'Na': 120e-3 * 1e4,
'K': 36e-3 * 1e4,
'KaF': 0e-3 * 1e4,
'SKCa': 5e-3 * 1e4,
'CaL': 10e-3 * 1e4
}
libraryName = '/library'
compType = 'Compartment'
# Create the compartment
neuron = moose.Neutral('/neuron')
squid = u.createCompartment(neuron, 'HHsquidswag', squid_l, squid_rad, RM, CM,
RA, initVm, Em)
# Set the axial resistance to match the one in the ionchannel.py file
# and set the container to be used for channel creation
squid.Ra = 1
container = squid.parent.path
# Create the external current to be applied to the compartment
squid_pulse = u.createPulse(squid, 'rollingWave', pulse_dur, pulse_amp,
pulse_delay1, pulse_delay2)
# Create the data tables necessary to run the model
data = moose.Neutral('/data')
squid_Vm, squid_current = u.createDataTables(squid, data, squid_pulse)
# Create the channels necessary for the giant squid axon and place them in a library
soma_rad = 10e-6
dend_l = 100e-6
dend_rad = 1e-6
RM = 2
CM = 0.01
RA = 10
Em = -65e-3
pulse_dur = 100e-3
pulse_amp = 0.1e-9
pulse_delay = 50e-3
# Create a neutral directory for the neuron
neuron = moose.Neutral('/neuron')
# Create the soma under the neuron directory
soma = u.createCompartment(neuron, 'swagginSoma', soma_l, soma_rad, RM, CM, RA,
Em)
# Create the dendritic compartments under the neuron directory
dend_branch = u.discretize(neuron, numDends, dend_l, dend_rad, RM, CM, RA, Em)
# Connect the soma to the first element of the dendritic branch
moose.connect(soma, 'axialOut', dend_branch[0], 'handleAxial')
# Create a pulse and connect it to the soma
soma_pulse = u.createPulse(soma, 'rollingWave', pulse_dur, pulse_amp,
pulse_delay)
# Create data tables to store the voltage for the soma and each compartment
# making up the dendritic branch
data = moose.Neutral('/data')
soma_Vm = u.createDataTables(soma, data)
soma_l = 30e-6
soma_rad = 10e-6
RM = 1
CM = 0.01
RA = 1
Em = -65e-3
pulse_dur = 100e-3
pulse_amp = 0.1e-9
pulse_delay1 = 50e-3
pulse_delay2 = 1e9
# Create a neutral directory for the neuron
neuron = moose.Neutral('/neuron')
# Create the soma and connect a pulse to it
l = u.createCompartment(neuron,'swagginWagon',soma_l,soma_rad,RM,CM,RA,Em)
n = u.createPulse(l,'rollingWave',pulse_dur,pulse_amp,pulse_delay1,pulse_delay2)
# Create a neutral directory for the data and create data tables for the soma
data = moose.Neutral('/data')
m = u.createDataTables(l,data)
# Set the clock so that all components of the simulation run appropriately
moose.setClock(4, simDt)
# Run the experiment
moose.reinit()
moose.start(simTime)
# Compute delta VM at the steady state
delta_Vm = l.Rm*n.level[0]*(1-np.exp(-0.3/(l.Rm*l.Cm)))
EREST_ACT = -70e-3 #: Resting membrane potential
Em = EREST_ACT + 10.613e-3
initVm = EREST_ACT
soma_l = 50e-6
soma_rad = 15e-6
dend_l = 100e-6
dend_rad = 1e-6
RM = 1 / (0.3e-3 * 1e4)
CM = 1e-6 * 1e4
RA = 2
# Create the soma and dendrite under the neutral neuron directory, and connect them to each other
neuron = moose.Neutral('/neuron')
soma = u.createCompartment(neuron, 'swagginSoma', soma_l, soma_rad, RM, CM, RA,
Em, Em)
dend = u.createCompartment(neuron, 'swagginDend', dend_l, dend_rad, RM, CM, RA,
Em, Em)
moose.connect(soma, 'axial', dend, 'raxial')
# Define dictionaries for the excitatory and inhibitory channels, and the pre-synaptic neurons
glu = {'name': 'glu', 'Gbar': 1e-8, 'tau1': 1e-3, 'tau2': 5e-3, 'erev': 0}
GABA = {
'name': 'GABA',
'Gbar': 1e-6,
'tau1': 3e-3,
'tau2': 5e-3,
'erev': -80e-3
}
presyn1 = {'name': 'presyn1', 'rate': 10, 'refractT': 1e-3, 'delay': 5e-3}
presyn2 = {'name': 'presyn2', 'rate': 0, 'refractT': 1e-3, 'delay': 5e-3}