def to_nineml(self):
model = ul.Model(name=self.label)
for cs in self.current_sources:
model.add_component(cs.to_nineml())
# needToDefineWhichCellsTheCurrentIsInjectedInto
# doWeJustReuseThePopulationProjectionIdiom="?"
main_group = ul.Network(name="Network")
_populations = self.populations[:]
_projections = self.projections[:]
for a in self.assemblies:
group = a.to_nineml()
for p in a.populations:
_populations.remove(p)
group.add(p.to_nineml())
for prj in self.projections:
if (prj.pre is a or prj.pre in a.populations) and \
(prj.post is a or prj.post in a.populations):
_projections.remove(prj)
group.add(prj.to_nineml())
model.add_group(group)
for p in _populations:
main_group.add(p.to_nineml())
for prj in _projections:
main_group.add(prj.to_nineml())
model.add_group(main_group)
model.check()
return model
def build_model(order=1000,
epsilon=0.1,
delay=1.5,
J=0.1,
theta=20.0,
tau=20.0,
tau_syn=0.1,
tau_refrac=2.0,
v_reset=10.0,
R=1.5,
g=5,
eta=2):
"""
Build a NineML representation of the Brunel (2000) network model.
Arguments:
g: relative strength of inhibitory synapses
eta: nu_ext / nu_thresh
Returns:
a nineml user layer Model object
"""
Ne = 4 * order # number of excitatory neurons
Ni = 1 * order # number of inhibitory neurons
Ce = int(epsilon * Ne) # number of excitatory synapses per neuron
Ci = int(epsilon * Ni) # number of inhibitory synapses per neuron
Cext = Ce # effective number of external synapses per neuron
scale_factor = psp_height(tau, R, tau_syn)
Jeff = J / scale_factor # (nA) synaptic weight
Je = Jeff # excitatory weights
Ji = -g * Je # inhibitory weights
Jext = Je # external weights
nu_thresh = theta / (Je * Ce * R * tau_syn) # threshold rate
nu_ext = eta * nu_thresh # external rate per synapse
input_rate = 1000.0 * nu_ext * Cext # mean input spiking rate
neuron_parameters = nineml.PropertySet(tau=(tau, ms),
v_threshold=(theta, mV),
refractory_period=(tau_refrac, ms),
v_reset=(v_reset, mV),
R=(R, Mohm))
psr_parameters = nineml.PropertySet(tau=(tau_syn, ms))
v_init = nineml.RandomDistributionComponent(
"uniform_rest_to_threshold",
CATALOG_URL + "randomdistribution/Uniform.xml#UniformDistribution",
{
'minimum': (0.0, unitless),
'maximum': (theta, unitless)
},
)
neuron_initial_values = {"v": (v_init, mV), "refractory_end": (0.0, ms)}
synapse_initial_values = {"a": (0.0, nA), "b": (0.0, nA)}
celltype = nineml.SpikingNodeType("nrn",
CATALOG_URL +
"neuron/LeakyIntegrateAndFire.xml",
neuron_parameters,
initial_values=neuron_initial_values)
tpoisson_init = nineml.RandomDistributionComponent(
"exponential_first_spike_time", CATALOG_URL +
"randomdistribution/Exponential.xml#ExponentialDistribution",
{"rate": (input_rate, unitless)})
ext_stim = nineml.SpikingNodeType(
"stim",
CATALOG_URL + "input/Poisson.xml",
nineml.PropertySet(rate=(input_rate, Hz)),
initial_values={"t_next": (tpoisson_init, ms)})
psr = nineml.SynapseType("syn",
CATALOG_URL + "postsynapticresponse/Alpha.xml",
psr_parameters,
initial_values=synapse_initial_values)
exc_cells = nineml.Population("Exc", Ne, celltype, positions=None)
inh_cells = nineml.Population("Inh", Ni, celltype, positions=None)
external = nineml.Population("Ext", Ne + Ni, ext_stim, positions=None)
all_cells = nineml.Selection("All",
nineml.Concatenate(exc_cells, inh_cells))
one_to_one = nineml.ConnectionRuleComponent(
"OneToOne", CATALOG_URL + "connectionrule/OneToOne.xml")
random_exc = nineml.ConnectionRuleComponent(
"RandomExc", CATALOG_URL + "connectionrule/RandomFanIn.xml",
{"number": (Ce, unitless)})
random_inh = nineml.ConnectionRuleComponent(
"RandomInh", CATALOG_URL + "connectionrule/RandomFanIn.xml",
{"number": (Ci, unitless)})
static_ext = nineml.ConnectionType("ExternalPlasticity",
CATALOG_URL + "plasticity/Static.xml",
nineml.PropertySet(weight=(Jext, nA)))
#initial_values={"weight": (Jext, nA)})
static_exc = nineml.ConnectionType("ExcitatoryPlasticity",
CATALOG_URL + "plasticity/Static.xml",
nineml.PropertySet(weight=(Je, nA)))
#initial_values={"weight": (Je, nA)})
static_inh = nineml.ConnectionType("InhibitoryPlasticity",
CATALOG_URL + "plasticity/Static.xml",
nineml.PropertySet(weight=(Ji, nA)))
#initial_values={"weight": (Ji, nA)})
input_prj = nineml.Projection(
"External",
external,
all_cells,
connectivity=one_to_one,
response=psr,
plasticity=static_ext,
port_connections=[
nineml.PortConnection("plasticity", "response", "fixed_weight",
"weight"),
nineml.PortConnection("response", "destination", "i_synaptic",
"i_synaptic")
],
delay=(delay, ms))
exc_prj = nineml.Projection(
"Excitation",
exc_cells,
all_cells,
connectivity=random_exc,
response=psr,
plasticity=static_exc,
port_connections=[
nineml.PortConnection("plasticity", "response", "fixed_weight",
"weight"),
nineml.PortConnection("response", "destination", "i_synaptic",
"i_synaptic")
],
delay=(delay, ms))
inh_prj = nineml.Projection(
"Inhibition",
inh_cells,
all_cells,
connectivity=random_inh,
response=psr,
plasticity=static_inh,
port_connections=[
nineml.PortConnection("plasticity", "response", "fixed_weight",
"weight"),
nineml.PortConnection("response", "destination", "i_synaptic",
"i_synaptic")
],
delay=(delay, ms))
network = nineml.Network("BrunelCaseC")
network.add(exc_cells, inh_cells, external, all_cells)
network.add(input_prj, exc_prj, inh_prj)
return network
def build_model(N=100,
delay=1.5,
weight=0.1,
theta=20.0,
tau=20.0,
tau_syn=0.1,
tau_refrac=2.0,
v_reset=10.0,
R=1.5,
interval=5.0):
"""
docstring missing
"""
neuron_parameters = nineml.PropertySet(tau=(tau, ms),
v_threshold=(theta, mV),
refractory_period=(tau_refrac, ms),
v_reset=(v_reset, mV),
R=(R, Mohm))
psr_parameters = nineml.PropertySet(tau=(tau_syn, ms))
v_init = v_reset
neuron_initial_values = {"v": (v_init, mV), "refractory_end": (0.0, ms)}
synapse_initial_values = {"a": (0.0, nA), "b": (0.0, nA)}
celltype = nineml.SpikingNodeType("nrn",
CATALOG_URL +
"neuron/LeakyIntegrateAndFire.xml",
neuron_parameters,
initial_values=neuron_initial_values)
ext_stim = nineml.SpikingNodeType("stim",
join(dirname(__file__), "Tonic.xml"),
nineml.PropertySet(interval=(interval,
ms)),
initial_values={"t_next": (10.0, ms)})
psr = nineml.SynapseType("syn",
CATALOG_URL + "postsynapticresponse/Alpha.xml",
psr_parameters,
initial_values=synapse_initial_values)
exc_cells = nineml.Population("Exc", N, celltype, positions=None)
external = nineml.Population("Ext", N, ext_stim, positions=None)
one_to_one = nineml.ConnectionRuleComponent(
"AllToAll", CATALOG_URL + "connectionrule/AllToAll.xml")
static_ext = nineml.ConnectionType("ExternalPlasticity",
CATALOG_URL + "plasticity/Static.xml",
nineml.PropertySet(weight=(weight, nA)))
input_prj = nineml.Projection(
"External",
external,
exc_cells,
connectivity=one_to_one,
response=psr,
plasticity=static_ext,
port_connections=[
nineml.PortConnection("plasticity", "response", "fixed_weight",
"weight"),
nineml.PortConnection("response", "destination", "i_synaptic",
"i_synaptic")
],
delay=(delay, ms))
network = nineml.Network("SimpleNetwork")
network.add(exc_cells, external)
network.add(input_prj)
return network