def main():
# Simulation information.
simtime = 0.1
simdt = 0.25e-5
plotdt = 0.25e-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
RA = 4
# Stimulus information
inj_delay = 20E-3
inj_amp = 1E-9
inj_width = 40E-3
# Create cell
chicken_model = create_swc_model(
root_name='E19',
file_name='E19-cell_filling-caudal.CNG.swc',
RM=RM,
CM=CM,
RA=RA,
ELEAK=Em,
initVM=Em)
soma = moose.element('/E19[0]/soma')
# Create channels
channels_set = create_set_of_channels(channel_settings, VDIVS, VMIN, VMAX)
# Fetch all compartment paths.
moose_paths = []
for comp in moose.wildcardFind(chicken_model.path +
'/#[TYPE=Compartment]'):
moose_paths.append(comp.path)
# Copy all channels to compartments.
for channel_name, channel_obj in channels_set.items():
copy_connect_channel_moose_paths(channel_obj, channel_name,
moose_paths)
# connect pulse gen
pulse_inject = create_pulse_generator(soma,
inj_width,
inj_amp,
delay=inj_delay)
# Output table
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somaIm')
chicken_dend_table = create_output_table(table_element='/output',
table_name='chkdend')
# Connect output tables
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(soma_i_table, 'requestOut', pulse_inject, 'getOutputValue')
moose.connect(chicken_dend_table, 'requestOut',
moose.element('/E19[0]/dend_36_0'), 'getVm')
# Set moose simulation clocks
for lable in range(7):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime,
soma_v_table,
soma_i_table,
chicken_dend_table,
title="soma vs dend new k1 chan g_bar = 0.05")
v_plot.legend(['soma_v', 'i', 'dend_v'])
plt.grid(True)
plt.show()
def main():
# Simulation information.
simtime = 0.1
simdt = 0.25e-5
plotdt = 0.25e-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
# Channel information.
sa, x_sa = compute_comp_area(diameter, length)
na_g = 120E-3 * sa * 1E4
na_ek = 115E-3 + EREST_ACT
k_g = 36e-3 * sa * 1E4
k_ek = -12E-3 + EREST_ACT
# Stimulus information
inj_delay = 20E-3
inj_amp = 1E-9
inj_width = 40E-3
# Create cell
soma = create_compartment('soma',
length,
diameter,
RM,
CM,
initVM=EREST_ACT,
ELEAK=Em)
# Create channels
k_chan = create_channel(chan_name='K',
vdivs=VDIVS,
vmin=VMIN,
vmax=VMAX,
x_params=K_n_params,
xpow=4)
Na_chan = create_channel(chan_name='Na',
vdivs=VDIVS,
vmin=VMIN,
vmax=VMAX,
x_params=Na_m_params,
xpow=3,
y_params=Na_h_params,
ypow=1)
# Set conductances
nachan = moose.copy(Na_chan, soma.path, 'Na', 1)
kchan = moose.copy(K_chan, soma.path, 'K', 1)
nachan = set_channel_conductance(nachan, na_g, na_ek)
kchan = set_channel_conductance(kchan, k_g, k_ek)
# Add channels to soma
moose.connect(nachan, 'channel', soma, 'channel', 'OneToOne')
moose.connect(kchan, 'channel', soma, 'channel', 'OneToOne')
# connect pulse gen
pulse_inject = create_pulse_generator(soma,
inj_width,
inj_amp,
delay=inj_delay)
# Output table
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somaIm')
# Connect output tables
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(soma_i_table, 'requestOut', pulse_inject, 'getOutputValue')
# Set moose simulation clocks
for lable in range(7):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime, "soma voltage", soma_v_table, soma_i_table)
plt.grid(True)
plt.legend(['v', 'i'])
plt.show()
def main(experiment_title):
# Simulation information.
simtime = 0.1
simdt = 0.25e-6
plotdt = 0.25E-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
# Stimulus information
inj_delay = 20E-3
inj_amp = 1E-9
inj_width = 40E-3
# Create cell
soma = create_compartment('soma',
length,
diameter,
RM,
CM,
initVM=EREST_ACT,
ELEAK=Em)
# Create channels
channels_set = create_set_of_channels(channel_settings, VDIVS, VMIN, VMAX,
CADIVS, CAMIN, CAMAX)
moose_paths = [soma.path]
for channel_name, channel_obj in channels_set.items():
copy_connect_channel_moose_paths(channel_obj, channel_name,
moose_paths)
# Create calcium pools in library.
ca_pool = create_ca_conc_pool(ca_params)
# copy calcium pools to all compartments.
copy_ca_pools_moose_paths(ca_pool, 'CaPool', moose_paths)
# Connect calciums pools to channels in compartments.
connect_ca_pool_to_chan(chan_name='SKca',
chan_type='ca_dependent',
calname='CaPool',
moose_paths=moose_paths)
connect_ca_pool_to_chan(chan_name='CaL',
chan_type='ca_permeable',
calname='CaPool',
moose_paths=moose_paths)
# connect pulse gen.
pulse_inject = create_pulse_generator(soma,
inj_width,
inj_amp,
delay=inj_delay)
# Output table.
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somaIm')
# Connect output tables.
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(soma_i_table, 'requestOut', pulse_inject, 'getOutputValue')
# Set moose simulation clocks.
for lable in range(10):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime,
soma_v_table,
soma_i_table,
title=experiment_title)
plt.grid(True)
plt.legend(['v', 'i'])
plt.show()
def main(model_name, comp_passive, channel_settings, ca_params):
# Simulation information.
simtime = 1
simdt = 0.25e-5
plotdt = 0.25e-3
diameter = 20e-6
length = 20e-6
# Model creation
soma, moose_paths = simple_model(model_name, comp_passive,
channel_settings, ca_params, length,
diameter)
# chirp_test = chirp(gen_name="chirp",amp=1E-9, f0=0.1, f1=500, T=0.8, start=inj_delay, end=inj_width+inj_delay, simdt=simdt,amp_offset=5E-9)
# moose.connect(chirp_test, 'valueOut', soma, 'injectMsg')
# Output table
tabs = creat_moose_tables()
# moose.connect(soma_i_table, 'requestOut', chirp_test, 'getValue')
# Set moose simulation clocks
for lable in range(7):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
#v_plot = plot_vm_table(simtime,soma_v_table, soma_i_table, title="soma vs i")
#plt.grid(True)
#plt.legend(['v', 'i'])
#plt.show()
# set conductance for a list to Ca_v1, Ca_V2 and CC
from collections import namedtuple
cond = namedtuple('cond', 'k Ltype Ntype cl')
test_conductances = [
cond(k=0.5E-3, Ltype=0.18E-3, Ntype=0.4E-3, cl=40E-3), # control test
cond(k=0.5E-3, Ltype=0.18E-3, Ntype=0,
cl=40E-3), # L-type frequecy reduce test
cond(k=0.5E-3, Ltype=0, Ntype=0.4E-3,
cl=40E-3), # N-type amplitude reduce test
cond(k=0.5E-3, Ltype=0.18E-3, Ntype=0.4E-3,
cl=0), # cl-type Current abolish test
cond(k=0.5E-3 * 0.2, Ltype=0.18E-3, Ntype=0.4E-3,
cl=40E-3) # K AHP reduce test
]
for K, V1, V2, cc in test_conductances:
moose.element('/soma/K').Gbar = K * compute_comp_area(
length, diameter)[0] * 1E4
moose.element('/soma/Ca_V1').Gbar = V1 * compute_comp_area(
length, diameter)[0] * 1E4
moose.element('/soma/Ca_V2').Gbar = V2 * compute_comp_area(
length, diameter)[0] * 1E4
moose.element('/soma/ca_cc').Gbar = cc * compute_comp_area(
length, diameter)[0] * 1E4
moose.reinit()
moose.start(simtime)
#plot_internal_currents(*tabs['internal_currents'])
plot_vm_table(
simtime,
tabs['vm'][0],
title=
'Conductances: ca_V1(L): {1}, Ca_V2 (N) :{0}, ca_cc :{2} K : {3}'.
format(V1, V2, cc, K),
xlab="Time in Seconds",
ylab="Volage (V)")
plt.show()
def main():
# Simulation information.
simtime = 0.1
simdt = 0.25e-5
plotdt = 0.25e-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
# Stimulus information
inj_delay = 20E-3
inj_amp = 1E-9
inj_width = 40E-3
# Create cell
soma = create_compartment('soma',
length,
diameter,
RM,
CM,
initVM=EREST_ACT,
ELEAK=Em)
# Create channels
channels_set = create_set_of_channels(channel_settings, VDIVS, VMIN, VMAX)
moose_paths = [soma.path]
for channel_name, channel_obj in channels_set.items():
copy_connect_channel_moose_paths(channel_obj, channel_name,
moose_paths)
# connect pulse gen
pulse_inject = create_pulse_generator(soma,
inj_width,
inj_amp,
delay=inj_delay)
# Output table
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
soma_i_table = create_output_table(table_element='/output',
table_name='somaIm')
# Connect output tables
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(soma_i_table, 'requestOut', pulse_inject, 'getOutputValue')
# Set moose simulation clocks
for lable in range(7):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime,
soma_v_table,
soma_i_table,
title="soma voltage")
plt.grid(True)
plt.legend(['v', 'i'])
plt.show()
def main(experiment_title, _rate, syn_g_max):
# Simulation information.
simtime = 1
simdt = 0.25e-6
plotdt = 0.25E-3
# Cell Compartment infromation
diameter = 30e-6
length = 50e-6
Em = EREST_ACT + 10.613e-3
CM = 1e-6 * 1e4
RM = 1 / (0.3E-3 * 1e4)
RA = 4
dend_n = 5
# Create two compartmental model.
soma = create_compartment('soma',
length,
diameter,
RM,
CM,
initVM=EREST_ACT,
ELEAK=Em) # Soma creation
bunch = create_n_dends('dend_', dend_n, length, diameter, RM, CM,
RA) # Dend creation
for item in bunch.values():
item.Em = Em
item.initVm = EREST_ACT
bunch = connect_n_serial(bunch)
moose.connect(soma, 'axial', list(bunch.values())[0], 'raxial')
# Create channels
channels_set = create_set_of_channels(channel_settings, VDIVS, VMIN, VMAX,
CADIVS, CAMIN, CAMAX)
# Create synaptic channel
synapses_and_handles = [
create_synaptic_channel(setting.syn_name, syn_g_max, setting.tau1,
setting.tau2, setting.ek,
setting.synapse_count, setting.delay)
for setting in synapse_settings
]
# Copy the synaptic channels to moose compartments.
moose_paths = [moose.element('/dend_2').path]
for syn, syn_handle in synapses_and_handles:
copy_syn_channel_moose_paths(syn, syn.name, moose_paths)
# create pre-synaptic input
spikegen_1 = create_spikegen(name='spikegen_1',
type='random',
refractory_period=1E-3,
rate=_rate)
moose.connect(spikegen_1, 'spikeOut',
moose.element('/dend_2[0]/syn[0]/synhandler').synapse[0],
'addSpike')
# connect channels to compartments.
for channel_name, channel_obj in channels_set.items(
): # Copy channels to soma.
copy_connect_channel_moose_paths(channel_obj, channel_name,
moose_paths)
# Output table.
soma_v_table = create_output_table(table_element='/output',
table_name='somaVm')
dend1_v_table = create_output_table(table_element='/output',
table_name='dend1Vm')
# Connect output tables.
moose.connect(soma_v_table, 'requestOut', soma, 'getVm')
moose.connect(dend1_v_table, 'requestOut', moose.element('/dend_2'),
'getVm')
# Set moose simulation clocks.
for lable in range(10):
moose.setClock(lable, simdt)
moose.setClock(8, plotdt)
# Run simulation
moose.reinit()
moose.start(simtime)
# Plot output tables.
v_plot = plot_vm_table(simtime,
soma_v_table,
dend1_v_table,
title=experiment_title.format(_rate, syn_g_max),
xlab='Time',
ylab='voltage')
plt.grid(True)
plt.legend(['soma', 'dend'])
plt.show()
