Example5.py

from neuromllite import Network, Cell, Synapse, NetworkReader, InputSource, Input
from neuromllite.NetworkGenerator import generate_neuroml2_from_network
import sys


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

percent = 5
net = Network(
    id="BBP_%spercent" % percent,
    notes="A network with the Blue Brain Project connectivity data (%s% of total cells)",
)

default_cell = Cell(id="hhcell", neuroml2_source_file="test_files/hhcell.cell.nml")

net.network_reader = NetworkReader(
    type="BBPConnectomeReader",
    parameters={
        "id": net.id,
        "filename": "test_files/cons_locs_pathways_mc0_Column.h5",
        "percentage_cells_per_pop": percent,
        "DEFAULT_CELL_ID": default_cell.id,
        "cell_info": {default_cell.id: default_cell},
    },
)

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


input_source = InputSource(
    id="poissonFiringSyn", neuroml2_source_file="test_files/inputs.nml"
)
net.input_sources.append(input_source)

for pop in ["L4_PC"]:
    net.inputs.append(
        Input(
            id="stim_%s" % pop,
            input_source=input_source.id,
            population=pop,
            percentage=80,
        )
    )

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


################################################################################
###   Builds a NeuroML 2 representation, save as XML

format_ = "xml"
nml_file_name, nml_doc = generate_neuroml2_from_network(
    net,
    nml_file_name="%s.net.nml%s" % (net.id, ".h5" if format_ == "hdf5" else ""),
    format=format_,
)


from neuromllite import Simulation

record_traces = {"all": "*"}
record_spikes = {"all": "*"}


sim = Simulation(
    id="SimExample5",
    network=new_file,
    duration=500,
    dt=0.025,
    record_traces=record_traces,
    record_spikes=record_spikes,
)

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)