def simulate_FSI_cell(par, par_sim):
pid = os.getpid()
b2.set_device('cpp_standalone', directory=join(
"output", f"standalone-{pid}"))
b2.get_device().reinit()
b2.get_device().activate(
directory=join("output", f"standalone-{pid}"))
num = par['num']
input_current = par['i_ext']
eqs = '''
Iapp = input_current(t, i): amp
m_inf = 1.0/(1.0+exp(-(vf+24*mV)/(11.5*mV))):1
h_inf = 1.0/(1.0+exp(-(vf+58.3*mV)/(-6.7*mV))):1
n_inf = 1.0/(1.0+exp(-(vf+12.4*mV)/(6.8*mV))):1
a_inf = 1.0/(1.0+exp(-(vf+50*mV)/(20.*mV))):1
b_inf = 1.0/(1.0+exp(-(vf+70*mV)/(-6.*mV))):1
tau_h=0.5*ms+14.0*ms/(1.0+exp(-(vf+60*mV)/(-12.*mV))):second
tau_n=(0.087*ms+11.4*ms/(1.0+exp(-(vf+14.6*mV)/(-8.6*mV))))
*(0.087+11.4/(1.0+exp(-(vf-1.3*mV)/(18.7*mV)))) :second
membrain_Im = -gNa*m_inf**3 *h*(vf-50*mV)
-gK*(n**power_n)*(vf+90*mV)
-gL*(vf+70*mV)-gA*a**3*b*(vf+90*mV)+Iapp:amp
dh/dt=(h_inf-h)/tau_h :1
dn/dt=(n_inf-n)/tau_n :1
da/dt=(a_inf-a)/(2.*ms) :1
db/dt=(b_inf-b)/(150.*ms) :1
dvf/dt=membrain_Im/Cm :volt
'''
neuron = b2.NeuronGroup(num,
eqs,
method=par_sim['integration_method'],
dt=par_sim['dt'],
threshold='vf>-20*mV',
refractory='vf>-20*mV',
namespace=par,
)
neuron.vf = par['v0']
neuron.h = "h_inf"
neuron.n = "n_inf"
neuron.a = "a_inf"
neuron.b = "b_inf"
st_mon = b2.StateMonitor(neuron, ["vf", "Iapp"], record=True)
net = b2.Network(neuron)
net.add(st_mon)
net.run(par_sim['simulation_time'])
return st_mon
def timed_run(self, duration):
'''
Do a timed run. This means that for RuntimeDevice it will run for defaultclock.dt before running for the
rest of the duration. This means total run duration will be duration+defaultclock.dt.
For standalone devices, this feature may or may not be implemented.
'''
if isinstance(brian2.get_device(), brian2.devices.RuntimeDevice):
brian2.run(brian2.defaultclock.dt, level=1)
brian2.run(duration, level=1)
else:
brian2.run(duration, level=1)
def timed_run(self, duration):
'''
Do a timed run. This means that for RuntimeDevice it will run for defaultclock.dt before running for the
rest of the duration. This means total run duration will be duration+defaultclock.dt.
For standalone devices, this feature may or may not be implemented.
'''
if isinstance(brian2.get_device(), brian2.devices.RuntimeDevice):
brian2.run(brian2.defaultclock.dt, level=1)
brian2.run(duration, level=1)
else:
brian2.run(duration, level=1)
def simulate(tau):
b2.start_scope()
if standalone_mode:
b2.get_device().reinit()
b2.get_device().activate(build_on_run=False, directory=directory_name)
net = b2.Network()
P = b2.PoissonGroup(num_inputs, rates=input_rate)
G = b2.NeuronGroup(1, eqs, threshold='v>1', reset='v=0', method='euler')
S = b2.Synapses(P, G, on_pre='v += weight')
S.connect()
M = b2.SpikeMonitor(G)
net.add(P)
net.add(G)
net.add(S)
net.add(M)
net.run(1000 * b2.ms)
if standalone_mode:
b2.get_device().build(directory=directory_name,
compile=True,
run=True,
debug=False)
return M
def __init__(self, filterbank, targetvar, *args, **kwds):
# Make sure we're not in standalone mode (which won't work)
if not isinstance(get_device(), RuntimeDevice):
raise RuntimeError("Cannot use standalone mode with brian2hears")
self.targetvar = targetvar
self.filterbank = filterbank
filterbank.buffer_init()
# Sanitize the clock - does it have the right dt value?
if 'clock' in kwds:
if int(1/kwds['clock'].dt)!=int(filterbank.samplerate):
raise ValueError('Clock should have 1/dt=samplerate')
elif 'dt' in kwds:
if int(1 / kwds['dt']) != int(filterbank.samplerate):
raise ValueError('Require 1/dt=samplerate')
else:
kwds['dt'] = 1/filterbank.samplerate
buffersize = kwds.pop('buffersize', 32)
if not isinstance(buffersize, int):
if not have_same_dimensions(buffersize, second):
raise DimensionMismatchError("buffersize argument should be an integer or in seconds")
buffersize = int(buffersize*filterbank.samplerate)
self.buffersize = buffersize
self.apply_filterbank = ApplyFilterbank(self, targetvar, filterbank, buffersize)
NeuronGroup.__init__(self, filterbank.nchannels, *args, **kwds)
if self.variables[targetvar].dim is not DIMENSIONLESS:
raise DimensionMismatchError("Target variable must be dimensionless")
apply_filterbank_output = NetworkOperation(self.apply_filterbank.__call__, when='start', clock=self.clock)
self.contained_objects.append(apply_filterbank_output)
def setup_fit():
"""
Function sets up simulator in one of the two available modes: runtime
or standalone. The `.Simulator` that will be used depends on the currently
set `.Device`. In the case of `.CPPStandaloneDevice`, the device will also
be reset if it has already run a simulation.
Returns
-------
simulator : `.Simulator`
"""
simulators = {
'CPPStandaloneDevice': CPPStandaloneSimulator(),
'RuntimeDevice': RuntimeSimulator()
}
if isinstance(get_device(), CPPStandaloneDevice):
if device.has_been_run is True:
get_device().reinit()
get_device().activate()
return simulators[get_device().__class__.__name__]
def network_sim():
# this line resets Brian's object tracking system, without it, the simulation will crash when run a second time
# bb.core.tracking.InstanceFollower.instance_sets = defaultdict(bb.core.tracking.InstanceTrackerSet)
bb.start_scope()
if faster_run:
bb.get_device().reinit()
bb.get_device().activate(build_on_run=False,
directory='PETH_standalone')
network = bb.Network()
Pe = bb.NeuronGroup(20000,
eqs_exc,
threshold='v > -50 * mV',
reset='v = -60 * mV',
refractory=2. * ms,
method='euler',
namespace=params)
# Pi = bb.NeuronGroup(5000, eqs_inh, threshold='v > -50 * mV',
# reset='v = -60 * mV', refractory=2. * ms, method='euler',
# namespace=params)
C_ee = bb.Synapses(Pe, Pe, model='w:siemens', on_pre='ge+=w')
#C_ie = bb.Synapses(Pe, Pi, model='w:siemens', on_pre='ge+=w')
i = np.random.randint(20000)
j = np.random.randint(20000)
C_ee.connect(i=i, j=j)
C_ee.w = params['g_ee']
network.add(Pe)
network.add(C_ee)
network.run(1 * second)
if faster_run:
bb.get_device().build(directory='PETH_standalone',
compile=True,
run=True,
debug=False)
return network
def simulate_MSN_cell(par, par_sim):
pid = os.getpid()
b2.set_device('cpp_standalone',
directory=join("output", f"standalone-{pid}"))
b2.get_device().reinit()
b2.get_device().activate(directory=join("output", f"standalone-{pid}"))
num = par['num']
input_current = par['iapp']
eqs = '''
Iapp = input_current(t): amp
am_Na = -0.1*(vm+28*mV)/(1*mV)/(exp(-0.1*(vm+28*mV)/(1*mV))-1) :1
Bm_Na = 4*exp(-(vm+53*mV)/(18.*mV)) :1
ah_Na = 0.07*exp(-(vm+51*mV)/(20.*mV)) :1
Bh_Na = 1/(1+exp(-0.1*(vm+21*mV)/(1.*mV))) :1
minf_Na = am_Na/(am_Na+Bm_Na) :1
dh_Na/dt= 5*(ah_Na*(1-h_Na)-Bh_Na*h_Na) * 1/ms :1
iNa = gnabar*minf_Na**3*h_Na*(vm - eNa) :amp
an_K = (-0.01*(vm+27*mV)/(1*mV)/(exp(-0.1*(vm+27*mV)/(1*mV))-1)) :1
Bn_K = 0.125*exp(-(vm+37*mV)/(80.*mV)) :1
dn_K/dt=5*(an_K*(1-n_K)-Bn_K * n_K) * 1/ms :1
iK = gkbar*n_K**4*(vm - eK) :amp
iLeak = gleak*(vm - eLeak) :amp
minf_Kir=1/(1+exp(-(vm+100*mV)/(-10.*mV))) :1
dm_Kir/dt = (minf_Kir - m_Kir) / tau_m_Kir :1
iKir = gkirbar*m_Kir*(vm - eKir) :amp
hinf_Kaf=1/(1+exp(-(vm+70.4*mV)/(-7.6*mV))) :1
minf_Kaf=1/(1+exp(-(vm+33.1*mV)/(7.5*mV))) :1
tau_m_Kaf = 1./tadj *1*ms :second
tau_h_Kaf = 25./tadj *1*ms :second
dm_Kaf/dt = (minf_Kaf - m_Kaf) / tau_m_Kaf :1
dh_Kaf/dt = (hinf_Kaf - h_Kaf) / tau_h_Kaf :1
iKaf = gkafbar * m_Kaf * h_Kaf*(vm - eKaf) :amp
minf_Kas=1/(1+exp(-(vm+25.6*mV)/(13.3*mV))) :1
hinf_Kas=1/(1+exp(-(vm+78.8*mV)/(-10.4*mV))) :1
tau_m_Kas=131.4/(exp(-(vm+37.4*mV)/(27.3*mV))+exp((vm+37.4*mV)/(27.3*mV)))/tadj *1*ms :second
tau_h_Kas=(1790+2930*exp(-((vm+38.2*mV)/(28*mV))**2)*((vm+38.2*mV)/(28*mV)))/tadj *1*ms :second
dm_Kas/dt = ( minf_Kas - m_Kas ) / tau_m_Kas :1
dh_Kas/dt = ( hinf_Kas - h_Kas ) / tau_h_Kas :1
iKas = gkasbar*m_Kas*h_Kas*(vm - eKas) :amp
minf_Krp=1/(1+exp(-(vm+13.4*mV)/(12.1*mV))) :1
hinf_Krp=1/(1+exp(-(vm+55*mV)/(-19*mV))) :1
tau_m_Krp=206.2/(exp(-(vm+53.9*mV)/(26.5*mV))+exp((vm+53.9*mV)/(26.5*mV)))/tadj *1*ms:second
tau_h_Krp=3*(1790+2930*exp(-((vm+38.2*mV)/(28*mV))**2)*((vm+38.2*mV)/(28*mV)))/tadj *1*ms :second
dm_Krp/dt = ( minf_Krp - m_Krp ) / tau_m_Krp :1
dh_Krp/dt = ( hinf_Krp - h_Krp ) / tau_h_Krp :1
iKrp = gkrpbar*m_Krp*h_Krp*(vm - eKrp) :amp
minf_Nap=1/(1+exp(-(vm+47.8*mV)/(3.1*mV))) :1
tau_m_Nap=1/tadj *1*ms:second
dm_Nap/dt = (minf_Nap - m_Nap) / tau_m_Nap :1
iNap = gnapbar*m_Nap*(vm - eNap) :amp
minf_Nas=1/(1+exp(-(vm+16*mV)/(9.4*mV))) :1
tau_m_Nas=637.8/(exp(-(vm+33.5*mV)/(26.3*mV))+exp((vm+33.5*mV)/(26.3*mV)))/tadj_Nas *1*ms:second
dm_Nas/dt = ( minf_Nas - m_Nas ) / tau_m_Nas :1
iNas = gnasbar * m_Nas *(vm - eNas) :amp
membrain_Im = Iapp-iLeak-iNa-iK-iKir-iKaf-iKrp-iNap-iNas-iKas :amp
dvm/dt = membrain_Im/Cm :volt
'''
neuron = b2.NeuronGroup(
num,
eqs,
method=par_sim['integration_method'],
dt=par_sim['dt'],
threshold='vm>-20*mV',
refractory='vm>-20*mV',
namespace=par,
)
neuron.vm = par['v0']
neuron.h_Na = 'ah_Na/(ah_Na + Bh_Na)' # 'hinf_Na'
neuron.n_K = 'an_K/(an_K + Bn_K)' # ninf_K
neuron.m_Kir = 'minf_Kir'
neuron.m_Kaf = 'minf_Kaf'
neuron.h_Kaf = 'hinf_Kaf'
neuron.m_Kas = 'minf_Kas'
neuron.h_Kas = 'hinf_Kas'
neuron.m_Krp = 'minf_Krp'
neuron.h_Krp = 'hinf_Krp'
neuron.m_Nap = 'minf_Nap'
neuron.m_Nas = 'minf_Nas'
st_mon = b2.StateMonitor(neuron, par['record_from'], record=True)
net = b2.Network(neuron)
net.add(st_mon)
net.run(par_sim['simulation_time'])
return st_mon
def simulate_GPe_cell(par, par_sim):
pid = os.getpid()
b2.set_device('cpp_standalone',
directory=join("output", f"standalone-{pid}"))
b2.get_device().reinit()
b2.get_device().activate(directory=join("output", f"standalone-{pid}"))
num = par['num']
if not par_sim['ADD_SPIKE_MONITOR']:
input_current = par['iapp']
eqs = '''
Iapp = input_current(t, i): amp
# Iapp :amp
minf_Naf = 1.0 / (1.0 + exp((-39*mV - vg)/(5*mV))) :1
hinf_Naf = 1.0 / (1.0 + exp(((-48*mV) - vg)/(-2.8*mV))) :1
sinf_Naf = 0.15 + (1.0 - 0.15)/(1.0 + exp((-40*mV - vg)/(-5.4*mV))) :1
tauh_Naf = 0.25*ms + (3.75*ms)/(exp((-43*mV - vg)/(10.*mV)) + exp((-43*mV - vg)/(-5*mV))) :second
taus_Naf = 10*ms + (990*ms)/(exp((-40*mV - vg)/(18.3*mV)) + exp((-40*mV - vg)/(-10*mV))) :second
dm_Naf/dt = (minf_Naf - m_Naf)/(0.028*ms) :1
dh_Naf/dt = (hinf_Naf - h_Naf)/tauh_Naf :1
ds_Naf/dt = (sinf_Naf - s_Naf)/taus_Naf :1
iNaf = gnafbar*m_Naf**3*h_Naf*s_Naf*(vg-eNa) :amp
minf_Nap = 1.0 / (1.0 + exp((-57.7*mV - vg)/(5.7*mV))) :1
hinf_Nap = 0.154 + (1.0 - 0.154)/ (1.0 + exp((-57*mV - vg)/(-4.*mV))) :1
# sinf_Nap = 1.0 / (1.0 + exp((-10*mV - vg)/(-4.9*mV))) :1
taum_Nap = 0.03*ms + (0.146*ms - 0.03*ms)/(exp((-42.6*mV - vg)/(14.4*mV)) + exp((-42.6*mV - vg)/(-14.4*mV))) :second
tauh_Nap = 10*ms + (7*ms)/(exp((-34*mV - vg)/(26.*mV)) + exp((-34*mV - vg)/(-31.9*mV))):second
# alphas_Nap = (-2.88e-6 * vg - 4.9e-5*mV)/mV/(1.0 - exp((vg + 17.014*mV)/(4.63*mV))) :1
# betas_Nap = 1/mV*(6.94e-6 * vg + 4.47e-4*mV)/(1.0 - exp((vg + (4.47e-4)/(6.94e-6) * 1*mV)/(2.63*mV))) :1
# taus_Nap = 1.0*ms / (alphas_Nap + betas_Nap) :second
dm_Nap/dt = (minf_Nap - m_Nap)/taum_Nap :1
dh_Nap/dt = (hinf_Nap - h_Nap)/tauh_Nap :1
# ds_Nap/dt = (sinf_Nap - s_Nap)/taus_Nap :1
# iNap = gnapbar*m_Nap**3*h_Nap*s_Nap*(vg-eNa) :amp
iNap = gnapbar*m_Nap**3*h_Nap*(vg-eNa) :amp
iLeak = gleak * (vg-eLeak) :amp
minf_Kv2 = 1.0 / (1.0 + exp((-33.2*mV - vg)/(9.1*mV))) :1
hinf_Kv2 = 0.2 + (0.8) / (1.0 + exp((-20*mV - vg)/(-10.*mV))) :1
taum_Kv2 = 0.1*ms + (2.9*ms)/(exp((-33.2*mV - vg)/(21.7*mV)) + exp((-33.2*mV - vg)/(-13.9*mV))) :second
dm_Kv2/dt = (minf_Kv2 - m_Kv2)/taum_Kv2 :1
dh_Kv2/dt = (hinf_Kv2 - h_Kv2)/(3400.*ms) :1
iKv2 = gkv2bar*m_Kv2*4*h_Kv2*(vg-eK) :amp
minf_Kv3 = 1.0 / (1.0 + exp((-26*mV - vg)/(7.8*mV))) :1
hinf_Kv3 = 0.6 + (0.4) / (1.0 + exp((-20*mV - vg)/(-10.*mV))) :1
taum_Kv3 = 0.1*ms + (13.9*ms)/(exp((-26*mV - vg)/(13.*mV)) + exp((-26*mV - vg)/(-12.*mV))) :second
tauh_Kv3 = 7*ms + (26*ms)/(exp((-vg)/(10*mV)) + exp((-vg)/(-10*mV))): second
dm_Kv3/dt = (minf_Kv3 - m_Kv3)/taum_Kv3 :1
dh_Kv3/dt = (hinf_Kv3 - h_Kv3)/tauh_Kv3 :1
iKv3 = gkv3bar*m_Kv3**4*h_Kv3*(vg-eK) :amp
# this is merged with kv4s
# minf_Kv4f = 1.0 / (1.0 + exp((-49*mV - vg)/(12.5*mV))) :1
# hinf_Kv4f = 1.0 / (1.0 + exp((-83*mV - vg)/(-10.*mV))) :1
# taum_Kv4f = 0.25*ms + (6.75*ms)/(exp((-49*mV - vg)/(29*mV)) + exp((-49*mV - vg)/(-29.*mV))) :second
# tauh_Kv4f = 7*ms + (14*ms)/(exp((-83*mV - vg)/(10*mV)) + exp((-83*mV - vg)/(-10.*mV))) :second
# dm_Kv4f/dt = (minf_Kv4f - m_Kv4f)/taum_Kv4f :1
# dh_Kv4f/dt = (hinf_Kv4f - h_Kv4f)/tauh_Kv4f :1
# iKv4f = gkv4fbar*m_Kv4f**4*h_Kv4f*(vg-eK) :amp
minf_Kv4s = 1.0 / (1.0 + exp((-49*mV - vg)/(12.5*mV))) :1
hinf_Kv4s = 1.0 / (1.0 + exp((-83*mV - vg)/(-10.*mV))) :1
taum_Kv4s = 0.25*ms + (6.75*ms)/(exp((-49*mV - vg)/(29*mV)) + exp((-49*mV - vg)/(-29.*mV))) :second
tauh_Kv4s = 15*ms + (85*ms)/(exp((-83*mV - vg)/(10*mV)) + exp((-83*mV - vg)/(-10.*mV))) :second
dm_Kv4s/dt = (minf_Kv4s - m_Kv4s)/taum_Kv4s :1
dh_Kv4s/dt = (hinf_Kv4s - h_Kv4s)/tauh_Kv4s :1
iKv4s = gkv4sbar*m_Kv4s**4*h_Kv4s*(vg-eK) :amp
minf_Kcnq = 1.0 / (1.0 + exp((-61*mV - vg)/(19.5*mV))) :1
taum_Kcnq = 6.7*ms + (93.3*ms)/(exp((-61*mV - vg)/(35.*mV)) + exp((-61*mV - vg)/(-25.*mV))) :second
dm_Kcnq/dt = (minf_Kcnq - m_Kcnq)/taum_Kcnq :1
iKcnq = gkcnqbar*m_Kcnq**4*(vg-eK) :amp
minf_Hcn = 1.0 / (1.0 + exp((-76.4*mV - vg)/(-3.3*mV))) :1
taumhcn = (3625*ms)/(exp((-76.4*mV - vg)/(6.56*mV)) + exp((-76.4*mV - vg)/(-7.48*mV))) :second
taum_Hcn = taumhcn * int(taumhcn >= 0.01*ms) + 0.01*ms * int(taumhcn < 0.01*ms):second
dm_Hcn/dt = (minf_Hcn - m_Hcn)/taum_Hcn :1
iHcn = ghcnbar*m_Hcn*(vg-eCat) :amp
minf_Cah = 1.0 / (1.0 + exp((-20*mV - vg)/(7.*mV))) :1
dm_Cah/dt = (minf_Cah - m_Cah)/(0.2*ms) :1
iCah = gcahbar*m_Cah*(vg-eCa) :amp
# Ca Concentration ----------------------------------------------
dc_Ca/dt = -iCah*3000/(2*96485)/(uA)*(molar/second)- 0.4/ms*(c_Ca - 0.00001*mmolar) : mmolar
# SK Current (Ca-dependent)
minf_Sk = c_Ca**4.6/(c_Ca**4.6 + Gcan50) :1
tau_m_Sk = (76*ms-72*ms*c_Ca/mmolar/5) * int(c_Ca/mmolar < 5.) + 4*ms * int(c_Ca/mmolar >= 5) :second
# tau_m_Sk = 4.0*ms:second
dm_Sk/dt = (minf_Sk - m_Sk) / tau_m_Sk :1
iSk = gskbar*m_Sk*(vg-eK) :amp
# membrain_Im = Iapp-iNaf-iNap-iLeak-iKv2-iKv3-iKv4s
# -iKcnq-iHcn-iCah-iSk :amp
membrain_Im = Iapp-iNaf-iLeak-iNap-iKv2-iKv3-iKv4s
-iKcnq-iHcn-iCah-iSk :amp
dvg/dt = membrain_Im/Cm :volt
'''
neuron = b2.NeuronGroup(
num,
eqs,
method=par_sim['integration_method'],
dt=par_sim['dt'],
threshold='vg>-20*mV',
refractory='vg>-20*mV',
namespace=par,
)
neuron.vg = par['v0']
neuron.m_Naf = 'minf_Naf'
neuron.h_Naf = 'hinf_Naf'
neuron.s_Naf = 'sinf_Naf'
neuron.m_Nap = 'minf_Nap'
neuron.h_Nap = 'hinf_Nap'
neuron.m_Kv2 = 'minf_Kv2'
neuron.h_Kv2 = 'hinf_Kv2'
neuron.m_Kv3 = 'minf_Kv3'
neuron.h_Kv3 = 'hinf_Kv3'
# neuron.m_Kv4f = 'minf_Kv4f'
# neuron.h_Kv4f = 'hinf_Kv4f'
neuron.m_Kv4s = 'minf_Kv4s'
neuron.h_Kv4s = 'hinf_Kv4s'
neuron.m_Kcnq = 'minf_Kcnq'
neuron.m_Hcn = 'minf_Hcn'
neuron.m_Cah = 'minf_Cah'
neuron.m_Sk = 'minf_Sk'
if par_sim['ADD_SPIKE_MONITOR']:
neuron.Iapp = par['iapp']
st_mon = b2.StateMonitor(neuron, par['record_from'], record=True)
if par_sim['ADD_SPIKE_MONITOR']:
sp_mon = b2.SpikeMonitor(neuron, variables='vg', record=True)
net = b2.Network(neuron)
net.add(st_mon)
if par_sim['ADD_SPIKE_MONITOR']:
net.add(sp_mon)
net.run(par_sim['simulation_time'])
if par_sim['ADD_SPIKE_MONITOR']:
return sp_mon, neuron
else:
return st_mon
def simulate_STN_GPe_population(params):
pid = os.getpid()
b2.set_device(
'cpp_standalone',
# build_on_run=False,
directory=join("output", f"standalone-{pid}"))
# b2.start_scope()
par_s = params['par_s']
par_g = params['par_g']
par_syn = params['par_syn']
par_sim = params['par_sim']
if par_sim['standalone_mode']:
b2.get_device().reinit()
b2.get_device().activate(
# build_on_run=False,
directory=join("output", f"standalone-{pid}"))
b2.defaultclock.dt = par_sim['dt']
eqs_s = '''
minf = 1/(1+exp(-(vs-thetam*mV)/(sigmam*mV))) : 1
hinf = 1/(1+exp(-(vs-thetah*mV)/(sigmah*mV))) : 1
ninf = 1/(1+exp(-(vs-thetan*mV)/(sigman*mV))) : 1
ainf = 1/(1+exp(-(vs-thetaa*mV)/(sigmaa*mV))) : 1
binf = 1/(1+exp((r-thetab)/sigmab))-1/(1+exp(-thetab/sigmab)) : 1
rinf = 1/(1+exp(-(vs-thetar*mV)/(sigmar*mV))) : 1
sinf = 1/(1+exp(-(vs-thetas*mV)/(sigmas*mV))) : 1
taun = taun0+taun1/(1+exp(-(vs-thn*mV)/(sigmant*mV))) : second
tauh = tauh0+tauh1/(1+exp(-(vs-thh*mV)/(sigmaht*mV))) : second
taur = taur0+taur1/(1+exp(-(vs-thr*mV)/(sigmart*mV))) : second
il = gl * (vs - vl) : amp
ina = gna * minf ** 3 * h * (vs - vna) : amp
ik = gk * n ** 4 * (vs - vk) : amp
iahp = gahp * ca / (ca + k1) * (vs - vk) : amp
ica = gca * sinf ** 2 * (vs - vca) : amp
it = gt * ainf ** 3 * binf ** 2 * (vs - vca) : amp
i_exts : amp
i_syn_GtoS : amp
s_GtoS_sum : 1
tmp2 = vs - thetag_s *mV : volt
# Hinf_s = 1 / (1 + exp(-(tmp2 - thetas*mV) / (sigmas*mV))) : 1
Hinf_s = 1 / (1 + exp(-(tmp2 - thetagH_s*mV) / (sigmagH_s*mV))) : 1
ds_StoG/dt = alphas * Hinf_s * (1 - s_StoG) - betas * s_StoG : 1
dh/dt = phi * (hinf - h) / tauh : 1
dn/dt = phi * (ninf - n) / taun : 1
dr/dt = phir * (rinf - r) / taur : 1
dca/dt = eps * ((-ica - it)/pA - kca* ca) : 1
membrane_Im = -(il + ina + ik + it + ica + iahp)+i_exts+i_syn_GtoS:amp
dvs/dt = membrane_Im/C : volt
'''
eqs_g = '''
i_extg : amp
ainfg = 1 / (1 + exp(-(vg - thetaag*mV) / (sigag*mV))) : 1
sinfg = 1 / (1 + exp(-(vg - thetasg*mV) / (sigsg*mV))) : 1
rinfg = 1 / (1 + exp(-(vg - thetarg*mV) / (sigrg*mV))) : 1
minfg = 1 / (1 + exp(-(vg - thetamg*mV) / (sigmg*mV))) : 1
ninfg = 1 / (1 + exp(-(vg - thetang*mV) / (signg*mV))) : 1
hinfg = 1 / (1 + exp(-(vg - thetahg*mV) / (sighg*mV))) : 1
taung = taun0g + taun1g / (1 + exp(-(vg - thngt*mV) / (sng*mV))) : second
tauhg = tauh0g + tauh1g / (1 + exp(-(vg - thhgt*mV) / (shg*mV))) : second
dhg/dt = phihg*(hinfg-hg)/tauhg : 1
dng/dt = phing*(ninfg-ng)/taung : 1
drg/dt = phig*(rinfg-rg)/taurg : 1
dcag/dt= epsg*((-icag-itg)/pA - kcag*cag) : 1
dvg/dt = membrane_Im / C : volt
tmp1 = vg - thetag_g *mV : volt
# Hinf_g = 1 / (1 + exp(-(tmp1 - thetasg*mV) / (sigsg*mV))) : 1
Hinf_g = 1 / (1 + exp(-(tmp1 - thetagH_g*mV) / (sigmagH_g*mV))) : 1
ds_GtoS/dt = alphag * (1 - s_GtoS) * Hinf_g - betag * s_GtoS : 1
itg = gtg * (ainfg ** 3) * rg * (vg - vcag) : amp
inag = gnag * (minfg ** 3) * hg * (vg - vnag) : amp
ikg = gkg * (ng ** 4) * (vg - vkg) : amp
iahpg = gahpg * (vg - vkg) * cag / (cag + k1g) : amp
icag = gcag * (sinfg ** 2) * (vg - vcag) : amp
ilg = glg * (vg - vlg) : amp
s_StoG_sum : 1
i_syn_StoG : amp
i_syn_GtoG : amp
membrane_Im =-(itg+inag+ikg+iahpg+icag+ilg)+i_extg+i_syn_StoG+i_syn_GtoG : amp
'''
eqs_syn_GtoS = '''
i_syn_GtoS_post = g_GtoS*s_GtoS_pre*(v_rev_GtoS-vs):amp (summed)
'''
eqs_syn_StoG = '''
i_syn_StoG_post = g_StoG*s_StoG_pre*(v_rev_StoG-vg):amp (summed)
'''
eqs_syn_GtoG = '''
i_syn_GtoG_post = g_GtoG*s_GtoS_pre*(v_rev_GtoG-vg):amp (summed)
'''
#---------------------------------------------------------------#
neurons_s = b2.NeuronGroup(
par_s['num'],
eqs_s,
method=par_sim['integration_method'],
dt=par_sim['dt'],
threshold='vs>-20*mV',
refractory='vs>-20*mV',
namespace={
**par_s,
**par_syn
},
)
#---------------------------------------------------------------#
neurons_g = b2.NeuronGroup(
par_g['num'],
eqs_g,
method=par_sim['integration_method'],
dt=par_sim['dt'],
threshold='vg>-20*mV',
refractory='vg>-20*mV',
namespace={
**par_g,
**par_syn
},
)
# ---------------------------------------------------------------
syn_GtoS = b2.Synapses(neurons_g,
neurons_s,
eqs_syn_GtoS,
method=par_sim['integration_method'],
dt=par_sim['dt'],
namespace=par_syn)
# ---------------------------------------------------------------
cols, rows = np.nonzero(par_syn['adj_GtoS'])
syn_GtoS.connect(i=rows, j=cols)
# syn_GtoS.connect(j='i')
# syn_GtoS.connect(j='k for k in range(i-1, i+2)', skip_if_invalid=True)
# ---------------------------------------------------------------
syn_StoG = b2.Synapses(neurons_s,
neurons_g,
eqs_syn_StoG,
method=par_sim['integration_method'],
dt=par_sim['dt'],
namespace=par_syn)
syn_StoG.connect(j='i')
# ---------------------------------------------------------------
syn_GtoG = b2.Synapses(neurons_g,
neurons_g,
eqs_syn_GtoG,
method=par_sim['integration_method'],
dt=par_sim['dt'],
namespace=par_syn)
# figure 5, T2002
cols, rows = np.nonzero(par_syn['adj_GtoG'])
syn_GtoG.connect(i=rows, j=cols)
# syn_GtoG.connect(p=par_syn['p_GtoG'], condition='i != j')
# ---------------------------------------------------------------
neurons_s.vs = par_s['v0']
neurons_s.h = "hinf"
neurons_s.n = "ninf"
neurons_s.r = "rinf"
neurons_s.ca = 0
neurons_s.i_exts = par_s['i_ext']
neurons_g.vg = par_g['v0']
neurons_g.hg = "hinfg"
neurons_g.ng = "ninfg"
neurons_g.rg = "rinfg"
neurons_g.cag = 0
neurons_g.i_extg = par_g['i_ext']
#---------------------------------------------------------------#
state_mon_s = b2.StateMonitor(neurons_s, ["vs", "i_syn_GtoS", "ca"],
record=True)
state_mon_g = b2.StateMonitor(neurons_g, ["vg", "i_syn_StoG", "cag"],
record=True)
spike_mon_s = b2.SpikeMonitor(neurons_s)
spike_mon_g = b2.SpikeMonitor(neurons_g)
lfp_stn = b2.PopulationRateMonitor(neurons_s)
lfp_gpe = b2.PopulationRateMonitor(neurons_g)
net = b2.Network(neurons_s, neurons_g, state_mon_g, spike_mon_s,
state_mon_s, spike_mon_g)
net.add(syn_GtoS)
net.add(syn_StoG)
net.add(syn_GtoG)
net.add(lfp_gpe)
net.add(lfp_stn)
net.run(par_sim['simulation_time'])
# if par_sim['standalone_mode']:
# b2.get_device().build(directory="output",
# compile=True,
# run=True,
# debug=False)
monitors = {
"state_stn": state_mon_s,
"state_gpe": state_mon_g,
"spike_stn": spike_mon_s,
"spike_gpe": spike_mon_g,
"lfp_stn": lfp_stn,
"lfp_gpe": lfp_gpe,
}
return monitors
