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_component():
inter_event_regime = al.Regime(
name="intereventregime",
time_derivatives=["dA/dt = -A/taur", "dB/dt = -B/taud"],
transitions=[
al.On('spikeinput',
do=["A = A + weight*factor", "B = B + weight*factor"])
])
dynamicsblock = al.DynamicsBlock(
aliases=[
"taupeak := taur*taud/(taud - taur)*log(taud/taur)",
"factor := 1/(exp(-taupeak/taud) - exp(-taupeak/taur))",
"gB := 1/(1 + mgconc*exp(-1*gamma*V)/beta)",
"g := gB*gmax*(B-A)",
"I := g * df",
"df := (E-V)",
],
state_variables=[al.StateVariable(o) for o in ('A', 'B')],
regimes=[inter_event_regime],
)
nmda = al.ComponentClass(name="NMDAPSR",
dynamicsblock=dynamicsblock,
analog_ports=[
al.RecvPort("V"),
al.SendPort("I"),
],
event_ports=[al.RecvEventPort('spikeinput')],
parameters=[
'taur', 'taud', 'gmax', 'mgconc', 'gamma',
'beta', 'E', 'weight'
])
return nmda
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
import nineml.abstraction_layer as al
cond_decay = al.Regime(name='default',
time_derivatives=["dg/dt = -g/tau"],
transitions=[al.On(al.InputEvent('spikeinput'), do="g = g + q")]
)
coba_syn = al.ComponentClass(
name="CoBaSynapse",
dynamics=al.DynamicsBlock(
regimes=[cond_decay],
aliases=["I := g*(E-V)"],
),
analog_ports=[al.RecvPort("V"), al.SendPort("I")]
)
]
ports = [nineml.ReducePort("Isyn", op="+")]
leaky_iaf = nineml.Component("deltaLIFid5", regimes=regimes, ports=ports)
# delta jump synapses
regimes = [
nineml.Regime(
"dv/dt = -g*v",
transitions=nineml.On(nineml.SpikeInputEvent, do="g+=W"),
)
]
ports = [nineml.RecvPort("W"), nineml.SendPort("Isyn = dv/dt")]
# can i even send dv/dt as a variable?
delta_syn = nineml.Component("delta_jump_id5", regimes=regimes, ports=ports)
# User layer connects
# leaky_iaf.ports['V'] -> delta_syn.ports['V']
# delta_syn.ports['Isyn'] -> leaky_iaf.ports['Isyn'] for multiple synapses (reduce port)
# Simulator attaches to SpikeInput and SpikeOutput ports for input and output.
# write to file object f if defined
c1 = leaky_iaf
try:
# This case is used in the test suite for examples.
c1.write(f)
"do/dt = -o/tau_minus",
"deps_r/dt = (1-eps_r)/tau_er",
"deps_o/dt = (1-eps_o)/tau_eo",
transitions=[nineml.On(nineml.PreEvent,
do=["W -= R * A_minus * eps_r * o * (W - Wmin) / (Wmax - Wmin),
"W = max(W,W_min)",
"r += eps_r",
"eps_r = 0.0",
nineml.PreEventRelay]),
nineml.On(nineml.PostEvent,
do=["W += R*A_plus*eps_o*r*(Wmax-W)/(Wmax-Wmin)",
"W = max(W,W_max)",
"o += eps_o",
"eps_o = 0.0"])]
)]
ports = [nineml.RecvPort("R"), nineml.SendPort("W")]
c1 = nineml.Component("RmulSTDPid7", regimes=regimes, ports=ports)
# write to file object f if defined
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "RmulSTDPid7"
c1.write(base + ".xml")
c2 = nineml.parse(base + ".xml")
assert c1 == c2
ports = [nineml.SendPort("V"), nineml.ReducePort("Isyn", op="+")]
leaky_iaf = nineml.Component("gLIFid8", regimes=regimes, ports=ports)
# alpha conductances
regimes = [
nineml.Regime(
"dg_a/dt = -g_a/tau_a",
"dg/dt = g_a - g/tau_a",
transitions=nineml.On(nineml.SpikeInputEvent, do="g+=W"),
)
]
ports = [
nineml.RecvPort("V"),
nineml.RecvPort("W"),
nineml.SendPort("Isyn = g(E-V)")
]
coba_syn = nineml.Component("alpha_cond_id8", regimes=regimes, ports=ports)
# User layer connects
# leaky_iaf.ports['V'] -> coba_syn.ports['V']
# coba_syn.ports['Isyn'] -> leaky_iaf.ports['Isyn'] for multiple synapses (reduce port)
# Simulator attaches to SpikeInput and SpikeOutput ports for input and output.
# write to file object f if defined
c1 = leaky_iaf
try:
inter_event_regime = nineml.Regime(transitions=nineml.On(
nineml.SpikeInputEvent,
do=["pfire = W/N", "p = rand()"],
to="probabilistic_regime"),
name="inter_event_regime")
probabilistic_regime = nineml.Regime(transitions=[
nineml.On("pfire >= p",
do=nineml.SpikeInputEventRelay,
to=inter_event_regime),
nineml.On("pfire < p", to=inter_event_regime)
],
name="probabilistic_regime")
ports = [nineml.RecvPort("W")]
# problems: assumes the presence of a decent rand function
prob_input = nineml.Component(
"prob_id8", regimes=[inter_event_regime, probabilistic_regime])
c1 = linear_poiss
# write to file object f if defined
try:
# This case is used in the test suite for examples.
c1.write(f)
except NameError:
import os
base = "LPNid8"
c1.write(base + ".xml")