Motor neron circuit for c302 (AS01, AS02, DA01, DA02, DB01, DD01, SMDDL, SMDDR)

c302_Motor.py

# Model of a neuromotor circuit


# To run:
#          python c302_Motor.py A   (uses parameters_A, requires jNeuroML to run)
# or
#          python c302_Motor.py B   (uses parameters_B, requires jNeuroML built from the
#                                     experimental branches to run: 'python getNeuroML experimental'
#                                     see https://github.com/NeuroML/jNeuroML)

from c302 import generate

from neuroml import PulseGenerator
from neuroml import ExplicitInput
from neuroml import GapJunction
import neuroml.writers as writers

import sys

def add_new_input(nml_doc, cell, delay, duration, amplitude):

    stim = PulseGenerator(id="stim_"+cell, delay=delay, duration=duration, amplitude=amplitude)

    nml_doc.pulse_generators.append(stim)

    populations_without_location = isinstance(params.elec_syn, GapJunction)

    target ="%s/0/%s"%(cell, params.generic_cell.id)
    if populations_without_location:
        target ="%s[0]"%(cell)
    exp_input = ExplicitInput(target=target, input=stim.id)

    nml_doc.networks[0].explicit_inputs.append(exp_input)

if __name__ == '__main__':

    parameter_set = sys.argv[1] if len(sys.argv)==2 else 'A'

    exec('import parameters_%s as params'%parameter_set)

    cells = ['AS1','AS2','DA1','DA2','DB1','DD1','SMDDL','SMDDR']
    cells_to_stimulate      = []

    reference = "c302_%s_Motor"%parameter_set

    nml_doc = generate(reference,
                       params,
                       cells=cells,
                       cells_to_stimulate=cells_to_stimulate,
                       duration=2800,
                       dt=0.1,
                       vmin=-72 if parameter_set=='A' else -52,
                       vmax=-48 if parameter_set=='A' else -28,
                       validate=(parameter_set!='B'))

    stim_amplitude = "0.35nA"
    add_new_input(nml_doc, "AS1", "100ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "AS2", "400ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "DA1", "700ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "DA2", "1000ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "DB1", "1300ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "DD1", "1600ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "SMDDL", "1900ms", "200ms", stim_amplitude)
    add_new_input(nml_doc, "SMDDR", "2200ms", "200ms", stim_amplitude)


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

    print("(Re)written network file to: "+nml_file)