def get_component():
subthreshold_regime = al.Regime(
name="subthreshold_regime",
time_derivatives=[
"dV/dt = (g_L*(E_L-V) + g_sfa*(E_sfa-V) + g_rr*(E_rr-V) + Isyn)/C",
"dg_sfa/dt = -g_sfa/tau_sfa",
"dg_rr/dt = -g_rr/tau_rr",
],
transitions=al.On("V> theta",
do=["g_sfa =g_sfa + q_sfa", "g_rr =g_rr + q_rr", "t_spike = t",
al.OutputEvent('spikeoutput')],
to="refractory_regime"),
)
refractory_regime = al.Regime(
name="refractory_regime",
transitions=al.On("t >= t_spike + t_ref",
to='subthreshold_regime'),
)
analog_ports = [al.SendPort("V"),
al.ReducePort("Isyn", reduce_op="+")]
c1 = al.ComponentClass("iaf_sfa_relref",
regimes=[subthreshold_regime, refractory_regime],
analog_ports=analog_ports,
)
return c1
def get_component():
subthreshold_regime = al.Regime(
name="subthreshold_regime",
time_derivatives=[
"dV/dt = (-gL*(V-vL) + Isyn)/C",
],
transitions=[
al.On("V> theta",
do=[
"t_spike = t", "V = V_reset",
al.OutputEvent('spikeoutput')
],
to="refractory_regime")
],
)
refractory_regime = al.Regime(
transitions=[al.On("t >= t_spike + t_ref", to='subthreshold_regime')],
name="refractory_regime")
analog_ports = [al.SendPort("V"), al.ReducePort("Isyn", reduce_op="+")]
c1 = al.ComponentClass("LeakyIAF",
regimes=[subthreshold_regime, refractory_regime],
analog_ports=analog_ports)
return c1
def get_component():
parameters = [
'C_m', 'g_L', 'E_L', 'Delta', 'V_T', 'S', 'tau_ref', 'tau_w', 'a', 'b'
]
aeIF = al.ComponentClass(
"aeIF",
regimes=[
al.Regime(
name="subthresholdregime",
time_derivatives=[
"dV/dt = -g_L*(V-E_L)/C_m + g_L*Delta*exp((V-V_T)/Delta-w/S)/C_m+ Isyn/C_m",
"dw/dt = (a*(V-E_L)-w)/tau_w",
],
transitions=al.On(
"V > V_T",
do=["V = E_L", "w = w + b",
al.OutputEvent('spikeoutput')],
to="refractoryregime"),
),
al.Regime(
name="refractoryregime",
transitions=al.On("t>=tspike+trefractory",
to="subthresholdregime"),
)
],
analog_ports=[al.ReducePort("Isyn", reduce_op="+")])
return aeIF
def get_component():
# Leaky iaf
regimes = [
al.Regime(
"dV/dt = (-gL*(V-vL) + Isyn)/C",
transitions=al.On(
"V>Vth", do=["tspike = t", "V = V_reset", al.OutputEvent('spikeoutput')], to="refractory-regime"),
name="sub-threshold-regime"
),
al.Regime(
transitions=al.On("t >= tspike + trefractory", to="sub-threshold-regime"),
name="refractory-regime"
)]
analog_ports = [al.SendPort("V"),
al.ReducePort("Isyn", reduce_op="+")]
leaky_iaf = al.ComponentClass("LeakyIAF", regimes=regimes, analog_ports=analog_ports)
# ampa
regimes = [
al.Regime(
"dg/dt = -g/tau",
transitions=al.On(al.SpikeInputEvent, do="g+=q")
)]
analog_ports = [al.RecvPort("V"),
al.SendPort("Isyn = g(E-V)")]
coba_syn = al.ComponentClass("CoBaSynapse", regimes=regimes, analog_ports=analog_ports)
def get_Izh_component():
subthreshold_regime = al.Regime(
name="subthreshold_regime",
time_derivatives=[
"dV/dt = 0.04*V*V + 5*V + 140.0 - U + Isyn",
"dU/dt = a*(b*V - U)",
],
transitions=[
al.On("V > theta",
do=[
"V = c",
"U = U+ d",
al.OutputEvent('spike'),
],
to='subthreshold_regime')
])
ports = [
al.AnalogSendPort("V"),
al.AnalogReducePort("Isyn", reduce_op="+")
]
c1 = al.DynamicsClass(name="Izhikevich",
regimes=[subthreshold_regime],
analog_ports=ports)
return c1
def get_component():
iaf = al.dynamics.DynamicsClass(
name="iaf",
regimes=[
al.Regime(
name="subthresholdregime",
time_derivatives=["dV/dt = ( gl*( vrest - V ) + ISyn)/(cm)"],
transitions=al.On("V > vthresh",
do=[
"tspike = t", "V = vreset",
al.OutputEvent('spikeoutput')
],
to="refractoryregime"),
),
al.Regime(
name="refractoryregime",
time_derivatives=["dV/dt = 0"],
transitions=[
al.On("t >= tspike + taurefrac", to="subthresholdregime")
],
)
],
state_variables=[
al.StateVariable('V'),
al.StateVariable('tspike'),
],
analog_ports=[
al.AnalogSendPort("V"),
al.AnalogReducePort("ISyn", reduce_op="+"),
],
event_ports=[
al.EventSendPort('spikeoutput'),
],
parameters=['cm', 'taurefrac', 'gl', 'vreset', 'vrest', 'vthresh'])
return iaf
def get_aeIF_component():
"""
Adaptive exponential integrate-and-fire neuron as described in
A. Destexhe, J COmput Neurosci 27: 493--506 (2009)
Author B. Kriener (Jan 2011)
## neuron model: aeIF
## variables:
## V: membrane potential
## w: adaptation variable
## parameters:
## C_m # specific membrane capacitance [muF/cm**2]
## g_L # leak conductance [mS/cm**2]
## E_L # resting potential [mV]
## Delta # steepness of exponential approach to threshold [mV]
## V_T # spike threshold [mV]
## S # membrane area [mum**2]
## trefractory # refractory time [ms]
## tspike # spike time [ms]
## tau_w # adaptation time constant
## a, b # adaptation parameters [muS, nA]
"""
parameters = [
'C_m', 'g_L', 'E_L', 'Delta', 'V_T', 'S', 'trefractory', 'tspike',
'tau_w', 'a', 'b'
]
aeIF = al.ComponentClass(
"aeIF",
regimes=[
al.Regime(
name="subthresholdregime",
time_derivatives=[
"dV/dt = -g_L*(V-E_L)/C_m + Isyn/C_m + g_L*Delta*exp((V-V_T)/Delta-w/S)/C_m",
"dw/dt = (a*(V-E_L)-w)/tau_w",
],
transitions=al.On(
"V > V_T",
do=["V = E_L", "w = w + b",
al.OutputEvent('spikeoutput')],
to="refractoryregime"),
),
al.Regime(
name="refractoryregime",
transitions=al.On("t>=tspike+trefractory",
to="subthresholdregime"),
)
],
analog_ports=[al.ReducePort("Isyn", reduce_op="+")])
return aeIF
def get_component():
regimes = [
al.Regime(
name="sub_threshold_regime",
time_derivatives=[
"dV/dt = (v_rest - V)/tau_m + (gE*(e_rev_E - V) + gI*(e_rev_I - V) + i_offset)/cm",
"dgE/dt = -gE/tau_syn_E",
"dgI/dt = -gI/tau_syn_I",
],
transitions=(
al.On("V > v_thresh",
do=[
"t_spike = t", "V = v_reset",
al.OutputEvent('spikeoutput')
],
to="refractory_regime"),
al.On('excitatory', do="gE=gE+q"),
al.On('inhibitory', do="gI=gI+q"),
),
),
al.Regime(
name="refractory_regime",
time_derivatives=[
"dgE/dt = -gE/tau_syn_E",
"dgI/dt = -gI/tau_syn_I",
],
transitions=(
al.On("t >= t_spike + tau_refrac", to="sub_threshold_regime"),
al.On('excitatoryspike', do="gE=gE+q"),
al.On('inhibitoryspike', do="gI=gI+q"),
),
)
]
analog_ports = [
al.SendPort("V"),
al.SendPort("gE"),
al.SendPort("gI"),
al.RecvPort("q")
]
c1 = al.ComponentClass("IF_cond_exp",
regimes=regimes,
analog_ports=analog_ports)
return c1
def get_component():
regimes = [
al.Regime(
name="subthreshold_regime",
time_derivatives=[
"dV/dt = 0.04*V*V + 5*V + 140.0 - U + Isyn",
"dU/dt = a*(b*V - U)"
],
transitions=[
al.On("V > theta",
do=["V = c", "U = U + d",
al.OutputEvent('spikeoutput')])
],
)
]
analog_ports = [al.SendPort("V"), al.ReducePort("Isyn", reduce_op="+")]
c1 = al.ComponentClass("Izhikevich",
regimes=regimes,
analog_ports=analog_ports)
return c1
import nineml.abstraction_layer as al
# Define a single regime, and specify the differential equations,
# and a transition when we reach spiking threshold:
regime = al.Regime(
name='defaultregime',
time_derivatives=[
'dV/dt = 0.04*V*V + 5*V + 140 -U + I', 'dU/dt = a*(b*V - U)'
],
transitions=[
al.On('V > a',
do=['V = c', 'U = U + d ',
al.OutputEvent('spikeoutput')])
])
# Create the ComponentClass, including the dynamics.
iz = al.ComponentClass(name="IzikevichNeuron",
parameters=['a', 'b', 'c', 'd'],
analog_ports=[
al.AnalogPort('I', mode='recv'),
al.AnalogPort('V', mode='send')
],
event_ports=[al.EventPort('spikeoutput', mode='send')],
dynamicsblock=al.DynamicsBlock(
regimes=[regime], state_variables=['V', 'U']))
"""
import nineml.abstraction_layer as al
from nineml.abstraction_layer.units import voltage, time, resistance, current
model = al.DynamicsClass(
name="BrunelIaF",
regimes=[
al.Regime(
name="subthresholdRegime",
time_derivatives=["dV/dt = (-V + R*Isyn)/tau"],
transitions=al.On("V > theta",
do=[
"t_rpend = t + tau_rp", "V = Vreset",
al.OutputEvent('spikeOutput')
],
to="refractoryRegime"),
),
al.Regime(
name="refractoryRegime",
time_derivatives=["dV/dt = 0"],
transitions=[
al.On(
"t > t_rpend",
#do=[al.OutputEvent('refractoryEnd')],
to="subthresholdRegime")
],
)
],
state_variables=[
import nineml.abstraction_layer as al
r1 = al.Regime(
name="sub-threshold-regime",
time_derivatives=["dV/dt = (-gL*(V-vL) + I)/C", ],
transitions=[al.On("V>Vth",
do=["tspike = t",
"V = V_reset",
al.OutputEvent('spike')],
to="refractory-regime"), ],
)
r2 = al.Regime(name="refractory-regime",
transitions=[al.On("t >= tspike + trefractory",
to="sub-threshold-regime"), ],
)
leaky_iaf = al.ComponentClass("LeakyIAF",
dynamicsblock=al.DynamicsBlock(
regimes=[r1, r2],
state_variables=['V', 'tspike'],
),
analog_ports=[al.AnalogPort("I", mode='recv')],
parameters=['C', 'V_reset', 'Vth', 'gL', 't', 'trefractory', 'vL'],
)
leaky_iaf.write("leaky_iaf.xml")