def main(inj_amp, outfile):
# 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 = float(inj_amp)
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)
#save
np.save(outfile, soma_v_table.vector)
B_A=0.125e3, B_B=0.0, B_C=0.0, B_D=0.0 - EREST_ACT, B_F=80e-3)
K1_n_params = AlphaBetaparams(
A_A=1, A_B=0, A_C=1.0, A_D=-20E-3, A_F=-4e-3,
B_A=1, B_B=0.0, B_C=1.0, B_D= -20E-3, B_F=4e-3)
Na_chan = copy(channel_param_template)
k_chan = copy(channel_param_template)
k1_chan = copy(channel_param_template)
Na_chan['chan_name']='Na'
Na_chan['x_params']= Na_m_params
Na_chan['y_params']= Na_h_params
Na_chan['x_pow']= 3
Na_chan['y_pow']= 1
Na_chan['g_max']= 120E-3 *compute_comp_area(30e-6, 50e-6)[0] *1E4
#Na_chan['g_max']= 0
Na_chan['e_k']= 115E-3 + EREST_ACT
k_chan['chan_name']= 'K'
k_chan['x_params']= K_n_params
k_chan['x_pow']= 4
k_chan['g_max']= 36e-3 *compute_comp_area(30e-6, 50e-6)[0] *1E4
#k_chan['g_max']= 0
k_chan['e_k']= -12E-3 + EREST_ACT
k1_chan['chan_name']= 'K1'
k1_chan['x_params']= K_n_params
k1_chan['x_pow']= 4
k1_chan['g_max']= 0.05 *compute_comp_area(30e-6, 50e-6)[0] *1E4
#k1_chan['g_max']= 0
B_B=71E3,
B_C=-1.0,
B_D=-4E-3,
B_F=5e-3)
Na_chan = copy(channel_param_template)
k_chan = copy(channel_param_template)
SKca_chan = copy(channel_param_template)
CaL_chan = copy(channel_param_template)
Na_chan['chan_name'] = 'Na'
Na_chan['x_params'] = Na_m_params
Na_chan['y_params'] = Na_h_params
Na_chan['x_pow'] = 3
Na_chan['y_pow'] = 1
Na_chan['g_max'] = 120E-3 * compute_comp_area(30e-6, 50e-6)[0] * 1E4
Na_chan['e_k'] = 115E-3 + EREST_ACT
k_chan['chan_name'] = 'K'
k_chan['x_params'] = K_n_params
k_chan['x_pow'] = 4
k_chan['g_max'] = 36e-3 * compute_comp_area(30e-6, 50e-6)[0] * 1E4
k_chan['e_k'] = -12E-3 + EREST_ACT
SKca_chan['chan_name'] = 'SKca'
SKca_chan['z_params'] = sk_z_params
SKca_chan['z_pow'] = 1
SKca_chan['g_max'] = 2E-6 * compute_comp_area(30e-6, 50e-6)[0] * 1E4
SKca_chan['g_max'] = 0
SKca_chan['e_k'] = -87E-3
SKca_chan['chan_type'] = 'ca_dependent'
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(experiment_title, ca_g_max, skca_g_max):
# 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
channel_settings['CaL']['g_max'] = ca_g_max * compute_comp_area(
diameter, length)[0] * 1E4
channel_settings['SKca']['g_max'] = skca_g_max * compute_comp_area(
diameter, length)[0] * 1E4
# 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.format(ca_g_max, skca_g_max),
xlab='Time',
ylab='voltage')
plt.grid(True)
plt.legend(['v', 'i'])
plt.show()
