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pgleesonpgleeson
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Merge pull request #69 from openworm/development
Add intial nmllite version
2 parents f36b01c + 49d0ccd commit 4fa3145

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‎.gitignore‎

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@@ -41,3 +41,15 @@ OpenWormMuscleModel.egg-info
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/NeuroML2/*_main.json
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arm64
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/NeuroML2/LEMS_NeuronMuscle_eden.py
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/NeuroML2/nmllite/CaPool.nml
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/NeuroML2/nmllite/IClamp_SingleCompMuscle.gv.png
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/NeuroML2/nmllite/IClamp_SingleCompMuscle.net.png
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/NeuroML2/nmllite/LEMS_Sim_IClamp_SingleCompMuscle.png
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/NeuroML2/nmllite/LEMS_Sim_IClamp_SingleCompMuscle.xml
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/NeuroML2/nmllite/Leak.channel.nml
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/NeuroML2/nmllite/*dat
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/NeuroML2/nmllite/SingleCompMuscle.cell.nml
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/NeuroML2/nmllite/ca_boyle.channel.nml
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/NeuroML2/nmllite/k_fast.channel.nml
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/NeuroML2/nmllite/k_slow.channel.nml
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/NeuroML2/nmllite/report.Sim_IClamp_SingleCompMuscle.txt

‎NeuroML2/nmllite/GenerateExamples.py‎

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from neuromllite import *
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from neuromllite.NetworkGenerator import *
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from neuromllite.utils import create_new_model
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import sys
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sys.path.append("..")
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def generate(cell, duration=45, config='IClamp',parameters = None):
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reference = "%s_%s"%(config, cell)
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cell_id = '%sCell'%cell
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cell_nmll = Cell(id=cell_id, neuroml2_source_file='../%s.cell.nml'%(cell))
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################################################################################
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### Add some inputs
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if 'IClamp' in config:
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if not parameters:
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parameters = {}
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parameters['stim_amp'] = '700pA'
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parameters['offset_stim_amp'] = '-120 pA'
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input_source0 = InputSource(id='iclamp_stim',
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neuroml2_input='PulseGenerator',
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parameters={'amplitude':'stim_amp', 'delay':'5ms', 'duration':'20ms'})
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input_source1 = InputSource(id='iclamp_offset',
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neuroml2_input='PulseGenerator',
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parameters={'amplitude':'offset_stim_amp', 'delay':'0ms', 'duration':'10000ms'})
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else:
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if not parameters:
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parameters = {}
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parameters['average_rate'] = '100 Hz'
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parameters['number_per_cell'] = '10'
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input_source0 = InputSource(id='pfs0',
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neuroml2_input='PoissonFiringSynapse',
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parameters={'average_rate':'average_rate',
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'synapse':syn_exc.id,
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'spike_target':"./%s"%syn_exc.id})
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sim, net = create_new_model(reference,
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duration,
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dt=0.025, # ms
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temperature=34, # degC
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default_region='Worm',
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parameters = parameters,
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cell_for_default_population=cell_nmll,
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input_for_default_population=input_source0)
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net.input_sources.append(input_source1)
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net.inputs.append(Input(id='input_offset',
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input_source=input_source1.id,
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population=net.populations[0].id,
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percentage=100))
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net.to_json_file()
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return sim, net
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if __name__ == "__main__":
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sim, net = generate('SingleCompMuscle', 45, config="IClamp")
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check_to_generate_or_run(sys.argv, sim)
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‎NeuroML2/nmllite/IClamp_SingleCompMuscle.json‎

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{
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"IClamp_SingleCompMuscle": {
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"version": "NeuroMLlite v0.5.9",
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"notes": "A network model: IClamp_SingleCompMuscle",
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"parameters": {
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"stim_amp": "700pA",
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"offset_stim_amp": "-120 pA"
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},
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"cells": {
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"SingleCompMuscleCell": {
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"neuroml2_source_file": "../SingleCompMuscle.cell.nml"
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}
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},
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"input_sources": {
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"iclamp_stim": {
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"parameters": {
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"amplitude": "stim_amp",
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"delay": "5ms",
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"duration": "20ms"
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},
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"neuroml2_input": "PulseGenerator"
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},
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"iclamp_offset": {
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"parameters": {
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"amplitude": "offset_stim_amp",
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"delay": "0ms",
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"duration": "10000ms"
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},
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"neuroml2_input": "PulseGenerator"
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}
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},
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"regions": {
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"Worm": {
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"x": 0.0,
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"y": 0.0,
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"z": 0.0,
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"width": 1000.0,
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"height": 100.0,
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"depth": 1000.0
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}
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},
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"populations": {
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"pop_SingleCompMuscleCell": {
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"size": 1,
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"component": "SingleCompMuscleCell",
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"properties": {
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"color": "0.8 0 0"
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},
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"random_layout": {
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"region": "Worm"
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}
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}
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},
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"inputs": {
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"Stim_iclamp_stim": {
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"input_source": "iclamp_stim",
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"population": "pop_SingleCompMuscleCell",
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"percentage": 100
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},
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"input_offset": {
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"input_source": "iclamp_offset",
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"population": "pop_SingleCompMuscleCell",
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"percentage": 100
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}
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},
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"temperature": 34.0
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}
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}

‎NeuroML2/nmllite/IClamp_SingleCompMuscle.net.nml‎

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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="IClamp_SingleCompMuscle">
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<notes>Generated by NeuroMLlite v0.5.9
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Generated network: IClamp_SingleCompMuscle
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Generation seed: 1234
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NeuroMLlite parameters:
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offset_stim_amp = -120 pA
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stim_amp = 700pA</notes>
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<include href="../SingleCompMuscle.cell.nml"/>
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<pulseGenerator id="iclamp_stim" delay="5ms" duration="20ms" amplitude="700pA"/>
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<pulseGenerator id="iclamp_offset" delay="0ms" duration="10000ms" amplitude="-120 pA"/>
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<network id="IClamp_SingleCompMuscle" type="networkWithTemperature" temperature="34.0degC">
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<notes>A network model: IClamp_SingleCompMuscle</notes>
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<property tag="recommended_dt_ms" value="0.025"/>
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<property tag="recommended_duration_ms" value="45.0"/>
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<population id="pop_SingleCompMuscleCell" component="SingleCompMuscleCell" size="1" type="populationList">
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<property tag="color" value="0.8 0 0"/>
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<property tag="region" value="Worm"/>
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<instance id="0">
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<location x="966.453535692138757" y="44.073259917535268" z="7.491470058587191"/>
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</instance>
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</population>
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<inputList id="Stim_iclamp_stim" population="pop_SingleCompMuscleCell" component="iclamp_stim">
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<input id="0" target="../pop_SingleCompMuscleCell/0/SingleCompMuscleCell" destination="synapses"/>
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</inputList>
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<inputList id="input_offset" population="pop_SingleCompMuscleCell" component="iclamp_offset">
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<input id="0" target="../pop_SingleCompMuscleCell/0/SingleCompMuscleCell" destination="synapses"/>
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</inputList>
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</network>
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</neuroml>

‎NeuroML2/nmllite/Sim_IClamp_SingleCompMuscle.json‎

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{
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"Sim_IClamp_SingleCompMuscle": {
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"version": "NeuroMLlite v0.5.9",
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"network": "IClamp_SingleCompMuscle.json",
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"duration": 45.0,
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"dt": 0.025,
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"seed": 12345,
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"record_traces": {
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"all": "*"
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}
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}
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}

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