Example11.py

from neuromllite import (
    Network,
    Cell,
    InputSource,
    Population,
    Synapse,
    RectangularRegion,
    RandomLayout,
)
from neuromllite import Projection, RandomConnectivity, Input, Simulation
import sys

################################################################################
###   Build new network

net = Network(id="Example11_Synapses")
net.notes = "Example 11: synaptic properties"
net.parameters = {"input_amp": 0.23, "weight": 1.01}
#'tau_syn':     2}

cell = Cell(id="iafCell0", neuroml2_source_file="test_files/iaf.cell.nml")
# cell.parameters = { "tau_refrac":5, "i_offset":0 }
net.cells.append(cell)


input_source = InputSource(
    id="i_clamp",
    pynn_input="DCSource",
    parameters={"amplitude": "input_amp", "start": 200.0, "stop": 800.0},
)
net.input_sources.append(input_source)

r1 = RectangularRegion(id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000)
net.regions.append(r1)

p0 = Population(
    id="pop0",
    size=1,
    component=cell.id,
    properties={"color": "1 0 0"},
    random_layout=RandomLayout(region=r1.id),
)
p1 = Population(
    id="pop1",
    size=1,
    component=cell.id,
    properties={"color": "0 1 0"},
    random_layout=RandomLayout(region=r1.id),
)

net.populations.append(p0)
net.populations.append(p1)

ampaSyn = Synapse(id="ampa", neuroml2_source_file="test_files/ampa.synapse.nml")
net.synapses.append(ampaSyn)

nmdaSyn = Synapse(id="nmdaSyn", neuroml2_source_file="test_files/NMDA.synapse.nml")
net.synapses.append(nmdaSyn)

net.projections.append(
    Projection(
        id="proj0",
        presynaptic=p0.id,
        postsynaptic=p1.id,
        synapse=ampaSyn.id,
        delay=0,
        weight="weight",
    )
)
net.projections[0].random_connectivity = RandomConnectivity(probability=1)

net.projections.append(
    Projection(
        id="proj1",
        presynaptic=p0.id,
        postsynaptic=p1.id,
        synapse=nmdaSyn.id,
        delay=0,
        weight="weight",
    )
)
net.projections[1].random_connectivity = RandomConnectivity(probability=1)


net.inputs.append(
    Input(id="stim", input_source=input_source.id, population=p0.id, percentage=100)
)

print(net.to_json())
new_file = net.to_json_file("%s.json" % net.id)


################################################################################
###   Build Simulation object & save as JSON

sim = Simulation(
    id="SimExample11",
    network=new_file,
    duration="1000",
    dt="0.01",
    record_traces={"all": "*"},
    record_variables={
        "synapses:%s:0/g" % ampaSyn.id: {"pop1": "*"},
        "synapses:%s:0/g" % nmdaSyn.id: {"pop1": "*"},
    },
    record_spikes={"pop0": "*"},
)

sim.to_json_file()


################################################################################
###   Run in some simulators

from neuromllite.NetworkGenerator import check_to_generate_or_run
import sys

check_to_generate_or_run(sys.argv, sim)