c302_Social.py

# Model of a decision making circuit

# See https://github.com/openworm/OpenWorm/issues/212

# To run:
#          python c302_Social.py A   (uses parameters_A, requires jNeuroML to run)
# or
#          python c302_Social.py B   (uses parameters_B, requires jNeuroML built from the
#                                     experimental branches to run: 'python getNeuroML experimental'
#                                     see https://github.com/NeuroML/jNeuroML)

import c302

import neuroml.writers as writers

import sys
import importlib


def setup(
    parameter_set,
    generate=False,
    duration=2500,
    dt=0.05,
    target_directory="examples",
    data_reader="SpreadsheetDataReader",
    param_overrides={},
    config_param_overrides={},
    verbose=True,
):
    ParameterisedModel = getattr(
        importlib.import_module("c302.parameters_%s" % parameter_set),
        "ParameterisedModel",
    )
    params = ParameterisedModel()

    cells = ["RMGR", "ASHR", "ASKR", "AWBR", "IL2R", "RMHR", "URXR"]
    cells_to_stimulate = []

    reference = "c302_%s_Social" % parameter_set

    nml_doc = None

    if generate:
        nml_doc = c302.generate(
            reference,
            params,
            cells=cells,
            cells_to_stimulate=cells_to_stimulate,
            duration=duration,
            dt=dt,
            target_directory=target_directory,
            param_overrides=param_overrides,
            verbose=verbose,
            data_reader=data_reader,
        )

    stim_amplitude = "5pA"
    c302.add_new_input(nml_doc, "RMGR", "100ms", "200ms", stim_amplitude, params)
    c302.add_new_input(nml_doc, "ASHR", "400ms", "200ms", stim_amplitude, params)
    c302.add_new_input(nml_doc, "ASKR", "700ms", "200ms", stim_amplitude, params)
    c302.add_new_input(nml_doc, "AWBR", "1000ms", "200ms", stim_amplitude, params)
    c302.add_new_input(nml_doc, "IL2R", "1300ms", "200ms", stim_amplitude, params)
    c302.add_new_input(nml_doc, "RMHR", "1600ms", "200ms", stim_amplitude, params)
    c302.add_new_input(nml_doc, "URXR", "1900ms", "200ms", stim_amplitude, params)

    nml_file = target_directory + "/" + reference + ".net.nml"
    writers.NeuroMLWriter.write(
        nml_doc, nml_file
    )  # Write over network file written above...

    c302.print_("(Re)written network file to: " + nml_file)

    return cells, cells_to_stimulate, params, [], nml_doc


if __name__ == "__main__":
    parameter_set = sys.argv[1] if len(sys.argv) == 2 else "A"

    setup(parameter_set, generate=True)