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‎NeuroML/LEMS_SomaTest2.xml‎

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<Lems>
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<!-- Specify which component to run -->
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<Target component="Sim_IClamp" reportFile="report.Soma.__SIMULATOR__.txt"/>
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<!-- Include core NeuroML2 ComponentType definitions -->
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<Include file="Cells.xml"/>
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<Include file="Networks.xml"/>
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<Include file="Simulation.xml"/>
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<Include file="PyNN.xml"/>
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<include href="leak.channel.nml"/>
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<include href="kqt1.channel.nml"/>
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<include href="CaDynamics.nml"/>
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<pulseGenerator id="stim" delay="100ms" duration="500ms" amplitude="5pA"/>
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<cell id="TestCell">
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<morphology id="morphology">
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<segment id="0" name="soma">
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<proximal x="0.0" y="0.0" z="0.0" diameter="12.922774419120067"/>
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<distal x="0.0" y="12.922774419120067" z="0.0" diameter="12.922774419120067"/>
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</segment>
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<segmentGroup id="soma_group" neuroLexId="GO:0043025">
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<notes>Default soma segment group for the cell</notes>
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<member segment="0"/>
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</segmentGroup>
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<segmentGroup id="all">
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<notes>Default segment group for all segments in the cell</notes>
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<member segment="0"/>
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</segmentGroup>
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</morphology>
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<biophysicalProperties id="biophys">
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<membraneProperties>
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<channelDensity id="leak_chans" ionChannel="leak" condDensity="0.00021247533768401888 S_per_cm2" erev="-89.57mV" ion="non_specific"/>
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<channelDensity id="kqt1_chans" ionChannel="kqt1" condDensity="0.000303536 S_per_cm2" erev="-80mV" ion="k"/>
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<spikeThresh value="0mV"/>
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<specificCapacitance value="1.5 uF_per_cm2"/>
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<initMembPotential value="-70mV"/>
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</membraneProperties>
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<intracellularProperties>
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<species id="ca" concentrationModel="CaDynamics_VA5" ion="ca" initialConcentration=".0001 mM" initialExtConcentration="2 mM"/>
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<resistivity value="0.1 kohm_cm"/>
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</intracellularProperties>
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</biophysicalProperties>
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</cell>
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<network id="TestNet" type="networkWithTemperature" temperature="6.3degC">
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<property tag="recommended_dt_ms" value="0.025"/>
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<property tag="recommended_duration_ms" value="11000.0"/>
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<population id="pop0" component="TestCell" size="1" type="populationList">
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<property tag="color" value="0 0.5 1"/>
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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="input0" population="pop0" component="stim">
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<input id="0" target="../pop0/0/TestCell" destination="synapses"/>
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</inputList>
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</network>
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<Simulation id="Sim_IClamp" length="700.0ms" step="0.01ms" target="TestNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
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<!--
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<Display id="pop_m_h" title="Plots of m" timeScale="1ms" xmin="-50.0" xmax="750" ymin="-.1" ymax="1.1">
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<Line id="egl19_m_q" quantity="pop0/0/TestCell/biophys/membraneProperties/egl19_chans/egl19/m/q" scale="1" color="#0534e4" timeScale="1ms"/>
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<Line id="egl19_h_q" quantity="pop0/0/TestCell/biophys/membraneProperties/egl19_chans/egl19/h/q" scale="1" color="#fff4e4" timeScale="1ms"/>
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<Line id="slo1egl19_m_egl19" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/m_egl19" scale="1" color="#ff3333" timeScale="1ms"/>
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<Line id="slo1egl19_m" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/q" scale="1" color="#ff33ff" timeScale="1ms"/>
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<Line id="slo1egl19_kcm2" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/kcm2" scale="1" color="#faaaaf" timeScale="1ms"/>
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<Line id="slo1egl19_kom2" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/kom2" scale="1" color="#444aaf" timeScale="1ms"/>
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<Line id="slo1egl19_kop2" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/kop2" scale="1" color="#4999af" timeScale="1ms"/>
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</Display>
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<Display id="pop_caConc" title="Plots of caConc" timeScale="1ms" xmin="-50.0" xmax="750" ymin="0" ymax="6e-4">
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<Line id="pop_ca" quantity="pop0/0/TestCell/caConc" scale="1" color="#ff4f33" timeScale="1ms"/>
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<Line id="caconc_eca" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/caConc" scale="1" color="#faaaaf" timeScale="1ms"/>
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</Display>
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<Display id="pop_eca" title="Plots of eca" timeScale="1ms" xmin="-50.0" xmax="750" ymin="0" ymax="130">
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<Line id="pop_ca" quantity="pop0/0/TestCell/biophys/membraneProperties/egl19_chans/erev" scale="1mV" color="#ff4f33" timeScale="1ms"/>
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<Line id="slo1egl19_eca" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/eca" scale="1" color="#faaaaf" timeScale="1ms"/>
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</Display>
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-->
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<Display id="pop_v" title="Plots of pop_v" timeScale="1ms" xmin="-50.0" xmax="750" ymin="-92" ymax="0">
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<Line id="v" quantity="pop0/0/TestCell/v" scale="1mV" color="#85ff96" timeScale="1ms"/>
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</Display>
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<OutputFile id="Sim_v_dat" fileName="Soma.v.dat">
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<OutputColumn id="pop_v" quantity="pop0/0/TestCell/v"/>
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</OutputFile>
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<!--
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<OutputFile id="pop_caConc_dat" fileName="Soma.ca.dat">
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<OutputColumn id="pop_caConc" quantity="pop0/0/TestCell/caConc"/>
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</OutputFile>
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<OutputFile id="pop_eca_dat" fileName="Soma.eca.dat">
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<OutputColumn id="pop_eca" quantity="pop0/0/TestCell/biophys/membraneProperties/egl19_chans/erev"/>
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</OutputFile>
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<OutputFile id="pop_chans" fileName="Soma.chans.dat">
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<OutputColumn id="0" quantity="pop0/0/TestCell/biophys/membraneProperties/egl19_chans/egl19/m/q"/>
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<OutputColumn id="1" quantity="pop0/0/TestCell/biophys/membraneProperties/egl19_chans/egl19/h/q"/>
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<OutputColumn id="2" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/m_egl19"/>
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<OutputColumn id="3" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/q"/>
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</OutputFile>
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<OutputFile id="pop_vars" fileName="Soma.vars.dat">
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<OutputColumn id="0" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/kcm2"/>
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<OutputColumn id="1" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/kom2"/>
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<OutputColumn id="2" quantity="pop0/0/TestCell/biophys/membraneProperties/slo1egl19_chans/slo1egl19/m/steadyState/kop2"/>
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</OutputFile>
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-->
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</Simulation>
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</Lems>

‎NeuroML/compare2.py‎

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from pyneuroml import pynml
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from pyneuroml.plot.Plot import generate_plot
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from matplotlib import pyplot as plt
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plots = {
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"Membrane potentials": ["Soma.v.dat", "../Soma.si.dat"],
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}
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for p in plots:
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files = plots[p]
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times = []
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xs = []
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labels = []
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linewidths = []
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d, indices = pynml.reload_standard_dat_file(files[0])
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for i in indices:
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if i != "t":
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times.append(d["t"])
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xs.append(d[i])
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labels.append("jnml %i" % i if len(d) > 2 else "jnml")
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linewidths.append(3)
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d, indices = pynml.reload_standard_dat_file(files[1])
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for i in indices:
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if i != "t":
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times.append(d["t"])
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xs.append(d[i])
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labels.append("nrn %i" % i if len(d) > 2 else "nrn")
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linewidths.append(1)
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generate_plot(
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times,
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xs,
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p,
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labels=labels,
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linewidths=linewidths,
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show_plot_already=False,
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)
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plt.show()

‎NeuroML/kqt1.channel.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="kqt1">
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<notes>An ion channel from cell AIY from Nicoletti et al. 2024</notes>
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<ionChannelHH id="kqt1" species="k" conductance="10 pS">
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<gate id="m" instances="1" type="gateHHtauInf">
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<timeCourse type="kqt1_m_tau"/>
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<gate id="s" instances="1" type="gateHHtauInf">
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<timeCourse type="kqt1_s_tau"/>
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<steadyState type="kqt1_s_inf"/>
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</gate>
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</ionChannelHH>
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</Dynamics>
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</ComponentType>
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<ComponentType name="kqt1_m_tau" extends="baseVoltageDepTime">
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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</Dynamics>
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</ComponentType>
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<ComponentType name="kqt1_s_inf" extends="baseVoltageDepVariable">
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="s1" dimension="none" value="0.41"/>
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value="(p1tskqt1+(p2tskqt1/(1+((V-p3tskqt1)/p4tskqt1)^2))) * TIME_SCALE"/>
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</Dynamics>
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</ComponentType>
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</neuroml>

‎NeuroML/test2.sh‎

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#!/bin/bash
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set -ex
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# Format the code
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ruff format *.py
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./clean.sh || true
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cd ..
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nrniv Test_Soma2.hoc
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cd -
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jnml LEMS_SomaTest2.xml -nogui
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python compare2.py

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