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Moving neuroml to subfolder
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‎.github/workflows/non_omv.yml‎

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on:
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push:
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branches: [ master, development, experimental ]
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branches: [ main, development, experimental ]
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pull_request:
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branches: [ master, development, experimental ]
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branches: [ main, development, experimental ]
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jobs:
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build:

‎.github/workflows/omv-ci.yml‎

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name: Continuous build using OMV
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on:
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push:
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branches: [ main, development, experimental ]
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pull_request:
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branches: [ main, development, experimental ]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: [ "3.12" ]
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engine: [ jNeuroML_validate ]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install OMV
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run: |
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pip install git+https://github.com/OpenSourceBrain/osb-model-validation
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pip install scipy sympy matplotlib cython pandas tables
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- name: Run OMV tests on engine ${{ matrix.engine }}
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run: |
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omv all -V --engine=${{ matrix.engine }}
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- name: OMV final version info
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run: |
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omv list -V # list installed engines
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env

‎NeuroML2/.test.validate.omt‎

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# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation
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# This test will validate NeuroML 2 files in the current directory using: jnml -validate
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target: "*.nml"
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engine: jNeuroML_validate

NeuroPAL_All_straightened.net.nml renamed to NeuroML2/NeuroPAL_All_straightened.net.nml

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c302_A_Full.net.nml renamed to NeuroML2/c302_A_Full.net.nml

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c302_D_Full.net.nml renamed to NeuroML2/c302_D_Full.net.nml

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BioParameter: unphysiological_offset_current_dur = 900 ms (SRC: Testing Full net, certainty 0)
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</notes>
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<include href="cell_C.xml"/>
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<include href="cells/ADAL_D.cell.nml"/>
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<include href="cells/ADAR_D.cell.nml"/>
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<include href="cells/ADEL_D.cell.nml"/>

c302_D_Pharyngeal.net.nml renamed to NeuroML2/c302_D_Pharyngeal.net.nml

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BioParameter: unphysiological_offset_current_dur = 200ms (SRC: Testing Pharyngeal, certainty 0)
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</notes>
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<include href="cell_C.xml"/>
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<include href="cells/I1L_D.cell.nml"/>
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<include href="cells/I1R_D.cell.nml"/>
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<include href="cells/I2L_D.cell.nml"/>

‎NeuroML2/cell_C.xml‎

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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_v2beta4.xsd" id="cell_C">
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<!-- Note: Not fully valid NML2: <customHGate> -->
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<!--
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Parameters C for c302 still under developemnt!!
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Subject to change without notice!!
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The fixed values for the parameters here will have to be replaced by parameters set in parameters_C.py &
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built using libNeuroML classes
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-->
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<ionChannel id="Leak" conductance="10pS" type="ionChannelPassive"/>
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<ionChannel id="k_fast" conductance="10pS" type="ionChannelHH" species="k">
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<notes>K fast channel from Boyle and Cohen 2008</notes>
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<gateHHtauInf id="p" instances="4">
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<timeCourse type="fixedTimeCourse" tau="2.25518 ms"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="7.42636 mV" midpoint="-8.05232 mV"/>
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</gateHHtauInf>
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<gateHHtauInf id="q" instances="1">
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<timeCourse type="fixedTimeCourse" tau="149.963 ms"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="-9.97468 mV" midpoint="-15.6456 mV"/>
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</gateHHtauInf>
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</ionChannel>
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<ionChannel id="k_slow" conductance="10pS" type="ionChannelHH" species="k">
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<notes>K slow channel from Boyle and Cohen 2008</notes>
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<gateHHtauInf id="n" instances="1">
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<timeCourse type="fixedTimeCourse" tau="25.0007 ms"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="15.8512 mV" midpoint="19.8741 mV"/>
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</gateHHtauInf>
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</ionChannel>
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<ionChannel id="ca_boyle" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>Ca channel from Boyle and Cohen 2008</notes>
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<gateHHtauInf id="e" instances="2">
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<timeCourse type="fixedTimeCourse" tau="0.100027 ms"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/>
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</gateHHtauInf>
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<gateHHtauInf id="f" instances="1">
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<timeCourse type="fixedTimeCourse" tau="150.88 ms"/>
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<!-- Note!!!
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f gate is "inactivation" a/c B&C 2008 p172
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but the scale value from Table A1 (kf) is positive (5mV), i.e. steady
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state is zero for v << midpoint and 1 for v >> midpoint
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Couple this with a very slow time course & the ion channel never
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conducts as e^2 x f is always ~0
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Using -5.03176mV NOT 5mV for k/scale to make this INACTIVATION
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This is suggested by the value used here:
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https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/MatlabSupport/Main_Version/data/input.csv#L20
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see also
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https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/PythonSupport/Main_Version/compareToNeuroML2.py
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-->
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<steadyState type="HHSigmoidVariable" rate="1" scale="-5.03176 mV" midpoint="25.1815 mV"/>
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</gateHHtauInf>
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<customHGate id="h" instances="1" alpha="0.282473" ca_half="6.41889e-8 mM" k="-1.00056e-8 mM"/>
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</ionChannel>
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<ionChannel id="ca_simple" conductance="10pS" type="ionChannelHH" species="ca">
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<notes>Simplified Ca channel</notes>
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<gateHHtauInf id="e" instances="2">
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<timeCourse type="fixedTimeCourse" tau="0.100027 ms"/>
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<steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/>
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</gateHHtauInf>
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</ionChannel>
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<ComponentType name="customHGate"
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extends="gateHHtauInf"
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description="Custom gate for h">
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<Parameter name="alpha" dimension="none"/>
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<Parameter name="k" dimension="concentration"/>
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<Parameter name="ca_half" dimension="concentration"/>
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<Constant name="SEC" dimension="time" value="1s"/>
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<Exposure name="tau" dimension="time"/>
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<Exposure name="inf" dimension="none"/>
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<Requirement name="caConc" dimension="concentration"/>
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<Dynamics>
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<DerivedVariable name="rateScale" exposure="rateScale" dimension="none" value="1"/>
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<DerivedVariable name="inf" dimension="none" exposure="inf" value="1 / (1 + (exp( (ca_half - caConc) / k)))"/>
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<DerivedVariable name="tau" dimension="time" exposure="tau" value="0 * SEC"/>
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<DerivedVariable name="q" exposure="q" dimension="none" value="inf"/>
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<DerivedVariable name="fcond" exposure="fcond" dimension="none" value="1 +((q-1) * alpha)"/>
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</Dynamics>
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</ComponentType>
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</neuroml>

cells/ADAL_D.cell.nml renamed to NeuroML2/cells/ADAL_D.cell.nml

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cells/ADAR_D.cell.nml renamed to NeuroML2/cells/ADAR_D.cell.nml

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