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Adding nmllite to generate figures 4C and 7B from paper
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| <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="Fig4C_AWCon"> | ||
| <notes>Generated by NeuroMLlite v0.5.9 | ||
| Generated network: Fig4C_AWCon | ||
| Generation seed: 1234</notes> | ||
| <include href="AWCon.cell.nml"/> | ||
| <pulseGenerator id="iclamp_stim_min4" delay="200ms" duration="500ms" amplitude="-4pA"/> | ||
| <pulseGenerator id="iclamp_stim_0" delay="200ms" duration="500ms" amplitude="0pA"/> | ||
| <pulseGenerator id="iclamp_stim_4" delay="200ms" duration="500ms" amplitude="4pA"/> | ||
| <pulseGenerator id="iclamp_stim_8" delay="200ms" duration="500ms" amplitude="8pA"/> | ||
| <pulseGenerator id="iclamp_stim_12" delay="200ms" duration="500ms" amplitude="12pA"/> | ||
| <pulseGenerator id="iclamp_stim_16" delay="200ms" duration="500ms" amplitude="16pA"/> | ||
| <pulseGenerator id="iclamp_stim_20" delay="200ms" duration="500ms" amplitude="20pA"/> | ||
| <network id="Fig4C_AWCon" type="networkWithTemperature" temperature="34.0degC"> | ||
| <notes>A network model: Fig4C_AWCon</notes> | ||
| <property tag="recommended_dt_ms" value="0.025"/> | ||
| <property tag="recommended_duration_ms" value="800.0"/> | ||
| <population id="pop_AWCon" component="AWCon" size="7" type="populationList"> | ||
| <property tag="color" value="0.8 0 0"/> | ||
| <property tag="region" value="Worm"/> | ||
| <instance id="0"> | ||
| <location x="966.453535692138757" y="44.073259917535268" z="7.491470058587191"/> | ||
| </instance> | ||
| <instance id="1"> | ||
| <location x="910.975962449124154" y="93.926899736376399" z="582.227573058949133"/> | ||
| </instance> | ||
| <instance id="2"> | ||
| <location x="671.563481487985086" y="8.393822683708397" z="766.480932791796249"/> | ||
| </instance> | ||
| <instance id="3"> | ||
| <location x="236.809775363117751" y="3.081402172660996" z="788.772717236283484"/> | ||
| </instance> | ||
| <instance id="4"> | ||
| <location x="346.088965597123092" y="62.328147503916853" z="615.815695103615212"/> | ||
| </instance> | ||
| <instance id="5"> | ||
| <location x="148.55463870828757" y="18.309064740993165" z="114.412969688687639"/> | ||
| </instance> | ||
| <instance id="6"> | ||
| <location x="14.618780486909122" y="48.675154060475833" z="964.901560916215658"/> | ||
| </instance> | ||
| </population> | ||
| <inputList id="input_iclamp_stim_min4" population="pop_AWCon" component="iclamp_stim_min4"> | ||
| <input id="0" target="../pop_AWCon/0/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_0" population="pop_AWCon" component="iclamp_stim_0"> | ||
| <input id="0" target="../pop_AWCon/1/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_4" population="pop_AWCon" component="iclamp_stim_4"> | ||
| <input id="0" target="../pop_AWCon/2/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_8" population="pop_AWCon" component="iclamp_stim_8"> | ||
| <input id="0" target="../pop_AWCon/3/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_12" population="pop_AWCon" component="iclamp_stim_12"> | ||
| <input id="0" target="../pop_AWCon/4/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_16" population="pop_AWCon" component="iclamp_stim_16"> | ||
| <input id="0" target="../pop_AWCon/5/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_20" population="pop_AWCon" component="iclamp_stim_20"> | ||
| <input id="0" target="../pop_AWCon/6/AWCon" destination="synapses"/> | ||
| </inputList> | ||
| </network> | ||
| </neuroml> |
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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="Fig7B_RMD"> | ||
| <notes>Generated by NeuroMLlite v0.5.9 | ||
| Generated network: Fig7B_RMD | ||
| Generation seed: 1234</notes> | ||
| <include href="RMD.cell.nml"/> | ||
| <pulseGenerator id="iclamp_stim_min2" delay="110ms" duration="50ms" amplitude="-2pA"/> | ||
| <pulseGenerator id="iclamp_stim_2" delay="110ms" duration="50ms" amplitude="2pA"/> | ||
| <pulseGenerator id="iclamp_stim_6" delay="110ms" duration="50ms" amplitude="6pA"/> | ||
| <pulseGenerator id="iclamp_stim_10" delay="110ms" duration="50ms" amplitude="10pA"/> | ||
| <pulseGenerator id="iclamp_hyp" delay="210ms" duration="20ms" amplitude="-15pA"/> | ||
| <network id="Fig7B_RMD" type="networkWithTemperature" temperature="34.0degC"> | ||
| <notes>A network model: Fig7B_RMD</notes> | ||
| <property tag="recommended_dt_ms" value="0.025"/> | ||
| <property tag="recommended_duration_ms" value="250.0"/> | ||
| <population id="pop_RMD" component="RMD" size="4" type="populationList"> | ||
| <property tag="color" value="0.8 0 0"/> | ||
| <property tag="region" value="Worm"/> | ||
| <instance id="0"> | ||
| <location x="966.453535692138757" y="44.073259917535268" z="7.491470058587191"/> | ||
| </instance> | ||
| <instance id="1"> | ||
| <location x="910.975962449124154" y="93.926899736376399" z="582.227573058949133"/> | ||
| </instance> | ||
| <instance id="2"> | ||
| <location x="671.563481487985086" y="8.393822683708397" z="766.480932791796249"/> | ||
| </instance> | ||
| <instance id="3"> | ||
| <location x="236.809775363117751" y="3.081402172660996" z="788.772717236283484"/> | ||
| </instance> | ||
| </population> | ||
| <inputList id="input_iclamp_stim_min2" population="pop_RMD" component="iclamp_stim_min2"> | ||
| <input id="0" target="../pop_RMD/0/RMD" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_2" population="pop_RMD" component="iclamp_stim_2"> | ||
| <input id="0" target="../pop_RMD/1/RMD" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_6" population="pop_RMD" component="iclamp_stim_6"> | ||
| <input id="0" target="../pop_RMD/2/RMD" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_stim_10" population="pop_RMD" component="iclamp_stim_10"> | ||
| <input id="0" target="../pop_RMD/3/RMD" destination="synapses"/> | ||
| </inputList> | ||
| <inputList id="input_iclamp_hyp" population="pop_RMD" component="iclamp_hyp"> | ||
| <input id="0" target="../pop_RMD/0/RMD" destination="synapses"/> | ||
| <input id="1" target="../pop_RMD/1/RMD" destination="synapses"/> | ||
| <input id="2" target="../pop_RMD/2/RMD" destination="synapses"/> | ||
| <input id="3" target="../pop_RMD/3/RMD" destination="synapses"/> | ||
| </inputList> | ||
| </network> | ||
| </neuroml> |
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| from neuromllite import * | ||
| from neuromllite.NetworkGenerator import * | ||
| from neuromllite.utils import create_new_model | ||
| import sys | ||
|
|
||
|
|
||
| def generate(cell, config, parameters=None): | ||
| reference = "%s_%s" % (config, cell) | ||
|
|
||
| cell_id = "%s" % cell | ||
| cell_nmll = Cell(id=cell_id, neuroml2_source_file="%s.cell.nml" % (cell)) | ||
|
|
||
| amps = [-4, 0, 4, 8, 12, 16, 20] | ||
| stim_delay = 100 | ||
| stim_dur = 500 | ||
| post_stim = 100 | ||
| extra_init = 100 | ||
|
|
||
| if cell == "RMD": | ||
| amps = [-2, 2, 6, 10] | ||
| stim_delay = 10 | ||
| stim_dur = 50 | ||
| post_stim = 90 | ||
| extra_init = 100 | ||
|
|
||
| sim, net = create_new_model( | ||
| reference, | ||
| duration=extra_init + stim_delay + stim_dur + post_stim, | ||
| dt=0.025, # ms | ||
| temperature=34, # degC | ||
| default_region="Worm", | ||
| parameters=parameters, | ||
| cell_for_default_population=cell_nmll, | ||
| ) | ||
|
|
||
| net.populations[0].size = len(amps) | ||
|
|
||
| for i in amps: | ||
| ins = InputSource( | ||
| id="iclamp_stim_%s" % str(i).replace("-", "min"), | ||
| neuroml2_input="PulseGenerator", | ||
| parameters={ | ||
| "amplitude": "%spA" % i, | ||
| "delay": "%sms" % (extra_init + stim_delay), | ||
| "duration": "%sms" % (stim_dur), | ||
| }, | ||
| ) | ||
| net.input_sources.append(ins) | ||
| net.inputs.append( | ||
| Input( | ||
| id="input_%s" % ins.id, | ||
| input_source=ins.id, | ||
| population=net.populations[0].id, | ||
| cell_ids=[amps.index(i)], | ||
| ) | ||
| ) | ||
| if config == "Fig7B": | ||
| hyp_amp = -15 | ||
| hyp_delay = 50 | ||
| hyp_dur = 20 | ||
| ins = InputSource( | ||
| id="iclamp_hyp", | ||
| neuroml2_input="PulseGenerator", | ||
| parameters={ | ||
| "amplitude": "%spA" % hyp_amp, | ||
| "delay": "%sms" % (extra_init + stim_delay + stim_dur + hyp_delay), | ||
| "duration": "%sms" % (hyp_dur), | ||
| }, | ||
| ) | ||
| net.input_sources.append(ins) | ||
| net.inputs.append( | ||
| Input( | ||
| id="input_%s" % ins.id, | ||
| input_source=ins.id, | ||
| population=net.populations[0].id, | ||
| percentage=100, | ||
| ) | ||
| ) | ||
|
|
||
| net.to_json_file() | ||
|
|
||
| return sim, net | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
|
|
||
| sim, net = generate("AWCon", config="Fig4C") | ||
|
|
||
| check_to_generate_or_run(sys.argv, sim) | ||
|
|
||
| sim, net = generate("RMD", config="Fig7B") | ||
|
|
||
| check_to_generate_or_run(sys.argv, sim) |
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| <Lems> | ||
|
|
||
| <!-- | ||
| This LEMS file has been automatically generated using PyNeuroML v1.2.15 (libNeuroML v0.6.0) | ||
| --> | ||
|
|
||
| <!-- Specify which component to run --> | ||
| <Target component="Sim_Fig4C_AWCon" reportFile="report.Sim_Fig4C_AWCon.txt"/> | ||
|
|
||
| <!-- Include core NeuroML2 ComponentType definitions --> | ||
| <Include file="Cells.xml"/> | ||
| <Include file="Networks.xml"/> | ||
| <Include file="Simulation.xml"/> | ||
|
|
||
| <Include file="PyNN.xml"/> | ||
| <Include file="Fig4C_AWCon.net.nml"/> | ||
| <Include file="AWCon.cell.nml"/> | ||
|
|
||
| <Simulation id="Sim_Fig4C_AWCon" length="800.0ms" step="0.025ms" target="Fig4C_AWCon" seed="12345"> <!-- Note seed: ensures same random numbers used every run --> | ||
| <Display id="pop_AWCon_v" title="Plots of pop_AWCon_v" timeScale="1ms" xmin="-80.0" xmax="880.0000000000001" ymin="-80" ymax="40"> | ||
| <Line id="pop_AWCon_0_AWCon_v" quantity="pop_AWCon/0/AWCon/v" scale="1mV" color="#d54f33" timeScale="1ms"/> | ||
| <Line id="pop_AWCon_1_AWCon_v" quantity="pop_AWCon/1/AWCon/v" scale="1mV" color="#0534e4" timeScale="1ms"/> | ||
| <Line id="pop_AWCon_2_AWCon_v" quantity="pop_AWCon/2/AWCon/v" scale="1mV" color="#98e752" timeScale="1ms"/> | ||
| <Line id="pop_AWCon_3_AWCon_v" quantity="pop_AWCon/3/AWCon/v" scale="1mV" color="#bca074" timeScale="1ms"/> | ||
| <Line id="pop_AWCon_4_AWCon_v" quantity="pop_AWCon/4/AWCon/v" scale="1mV" color="#632794" timeScale="1ms"/> | ||
| <Line id="pop_AWCon_5_AWCon_v" quantity="pop_AWCon/5/AWCon/v" scale="1mV" color="#8a5d88" timeScale="1ms"/> | ||
| <Line id="pop_AWCon_6_AWCon_v" quantity="pop_AWCon/6/AWCon/v" scale="1mV" color="#df5954" timeScale="1ms"/> | ||
| </Display> | ||
|
|
||
| <OutputFile id="Sim_Fig4C_AWCon_pop_AWCon_v_dat" fileName="Sim_Fig4C_AWCon.pop_AWCon.v.dat"> | ||
| <OutputColumn id="pop_AWCon_0_AWCon_v" quantity="pop_AWCon/0/AWCon/v"/> | ||
| <OutputColumn id="pop_AWCon_1_AWCon_v" quantity="pop_AWCon/1/AWCon/v"/> | ||
| <OutputColumn id="pop_AWCon_2_AWCon_v" quantity="pop_AWCon/2/AWCon/v"/> | ||
| <OutputColumn id="pop_AWCon_3_AWCon_v" quantity="pop_AWCon/3/AWCon/v"/> | ||
| <OutputColumn id="pop_AWCon_4_AWCon_v" quantity="pop_AWCon/4/AWCon/v"/> | ||
| <OutputColumn id="pop_AWCon_5_AWCon_v" quantity="pop_AWCon/5/AWCon/v"/> | ||
| <OutputColumn id="pop_AWCon_6_AWCon_v" quantity="pop_AWCon/6/AWCon/v"/> | ||
| </OutputFile> | ||
|
|
||
| </Simulation> | ||
|
|
||
| </Lems> |
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|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| <Lems> | ||
|
|
||
| <!-- | ||
| This LEMS file has been automatically generated using PyNeuroML v1.2.15 (libNeuroML v0.6.0) | ||
| --> | ||
|
|
||
| <!-- Specify which component to run --> | ||
| <Target component="Sim_Fig7B_RMD" reportFile="report.Sim_Fig7B_RMD.txt"/> | ||
|
|
||
| <!-- Include core NeuroML2 ComponentType definitions --> | ||
| <Include file="Cells.xml"/> | ||
| <Include file="Networks.xml"/> | ||
| <Include file="Simulation.xml"/> | ||
|
|
||
| <Include file="PyNN.xml"/> | ||
| <Include file="Fig7B_RMD.net.nml"/> | ||
| <Include file="RMD.cell.nml"/> | ||
|
|
||
| <Simulation id="Sim_Fig7B_RMD" length="250.0ms" step="0.025ms" target="Fig7B_RMD" seed="12345"> <!-- Note seed: ensures same random numbers used every run --> | ||
| <Display id="pop_RMD_v" title="Plots of pop_RMD_v" timeScale="1ms" xmin="-25.0" xmax="275.0" ymin="-80" ymax="40"> | ||
| <Line id="pop_RMD_0_RMD_v" quantity="pop_RMD/0/RMD/v" scale="1mV" color="#d54f33" timeScale="1ms"/> | ||
| <Line id="pop_RMD_1_RMD_v" quantity="pop_RMD/1/RMD/v" scale="1mV" color="#0534e4" timeScale="1ms"/> | ||
| <Line id="pop_RMD_2_RMD_v" quantity="pop_RMD/2/RMD/v" scale="1mV" color="#98e752" timeScale="1ms"/> | ||
| <Line id="pop_RMD_3_RMD_v" quantity="pop_RMD/3/RMD/v" scale="1mV" color="#bca074" timeScale="1ms"/> | ||
| </Display> | ||
|
|
||
| <OutputFile id="Sim_Fig7B_RMD_pop_RMD_v_dat" fileName="Sim_Fig7B_RMD.pop_RMD.v.dat"> | ||
| <OutputColumn id="pop_RMD_0_RMD_v" quantity="pop_RMD/0/RMD/v"/> | ||
| <OutputColumn id="pop_RMD_1_RMD_v" quantity="pop_RMD/1/RMD/v"/> | ||
| <OutputColumn id="pop_RMD_2_RMD_v" quantity="pop_RMD/2/RMD/v"/> | ||
| <OutputColumn id="pop_RMD_3_RMD_v" quantity="pop_RMD/3/RMD/v"/> | ||
| </OutputFile> | ||
|
|
||
| </Simulation> | ||
|
|
||
| </Lems> |