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Merge pull request #15 from OpenSourceBrain/development
Adding <spikeThresh> for future nml validity
2 parents 2413bba + 406fc17 commit ead235a

32 files changed

+579
-561
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‎.github/workflows/non_omv.yml‎

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python-version: [ 3.7, 3.9 ]
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steps:
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- uses: actions/checkout@v2
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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@v2
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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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‎.github/workflows/omv-ci.yml‎

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jobs:
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build:
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runs-on: ubuntu-latest
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name: Py${{ matrix.python-version }}, ${{ matrix.engine}} on ${{ matrix.runs-on }}
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runs-on: ${{ matrix.runs-on }}
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strategy:
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fail-fast: false
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matrix:
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python-version: [ 3.9 ]
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python-version: [ "3.10" ]
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engine: [ NEURON, jNeuroML, jNeuroML_NEURON, jNeuroML_NetPyNE, jNeuroML_EDEN, jNeuroML_validate ]
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runs-on: [ubuntu-latest, macos-latest ]
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steps:
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- uses: actions/checkout@v3
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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@v4
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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 HDF5 for pytables on macos-latest
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if: ${{ matrix.runs-on == 'macos-latest' }}
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run: |
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brew install hdf5
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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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- 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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more NMC/NeuroML2/report*
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- name: OMV final version info
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run: |

‎NMC/NeuroML2/.test.jnmleden.omt‎

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spike detection:
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method: threshold
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threshold: 0
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tolerance: 0.000860873175366194
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tolerance: 0.000860898645740264

‎NMC/NeuroML2/LEMS_L1_HAC_cNAC187_1.xml‎

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<Lems>
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<!--
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This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
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This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
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-->
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<!-- Specify which component to run -->
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<Target component="L1_HAC_cNAC187_1" reportFile="report.l1.__SIMULATOR__.txt"/>
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<Target component="L1_HAC_cNAC187_1" reportFile="report.L1_HAC.__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="cNAC187_L1_HAC_f8c9772d9d.stepcurrent3.net.nml"/>
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<Include file="cNAC187_L1_HAC_f8c9772d9d_0_0.cell.nml"/>
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<Include file="K_Tst.channel.nml"/>
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<Include file="CaDynamics_E2_NML2.nml"/>
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<Include file="Ca_LVAst.channel.nml"/>
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<Include file="Ca.channel.nml"/>
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<Simulation id="L1_HAC_cNAC187_1" length="3000ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Simulation id="L1_HAC_cNAC187_1" length="3000.0ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Display id="DispPop__Pop_cNAC187_L1_HAC_f8c9772d9d_0_0" title="Membrane potentials of cells in Pop_cNAC187_L1_HAC_f8c9772d9d_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
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<Line id="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0[0]: v" quantity="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0/0/cNAC187_L1_HAC_f8c9772d9d_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
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</Display>
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<OutputFile id="Volts_file__Pop_cNAC187_L1_HAC_f8c9772d9d_0_0" fileName="L1_HAC_cNAC187_1.Pop_cNAC187_L1_HAC_f8c9772d9d_0_0.v.dat">
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<OutputColumn id="v_Pop_cNAC187_L1_HAC_f8c9772d9d_0_0_0_cNAC187_L1_HAC_f8c9772d9d_0_0_v" quantity="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0/0/cNAC187_L1_HAC_f8c9772d9d_0_0/v"/>
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<OutputColumn id="v_Pop_cNAC187_L1_HAC_f8c9772d9d_0_0_0_cNAC187_L1_HAC_f8c9772d9d_0_0_v" quantity="Pop_cNAC187_L1_HAC_f8c9772d9d_0_0/0/cNAC187_L1_HAC_f8c9772d9d_0_0/v"/>
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</OutputFile>
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</Simulation>
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</Lems>

‎NMC/NeuroML2/LEMS_L23_LBC_cSTUT189_1.xml‎

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<Lems>
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<!--
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This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
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This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
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-->
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<!-- Specify which component to run -->
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<Target component="L23_LBC_cSTUT189_1" reportFile="report.lbc.__SIMULATOR__.txt"/>
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<Target component="L23_LBC_cSTUT189_1" reportFile="report.L23_LBC.__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="cSTUT189_L23_LBC_e6e8f83407.stepcurrent3.net.nml"/>
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<Include file="cSTUT189_L23_LBC_e6e8f83407_0_0.cell.nml"/>
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<Include file="K_Tst.channel.nml"/>
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<Include file="CaDynamics_E2_NML2.nml"/>
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<Include file="Ca_LVAst.channel.nml"/>
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<Include file="Ca.channel.nml"/>
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<Simulation id="L23_LBC_cSTUT189_1" length="3000ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Simulation id="L23_LBC_cSTUT189_1" length="3000.0ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Display id="DispPop__Pop_cSTUT189_L23_LBC_e6e8f83407_0_0" title="Membrane potentials of cells in Pop_cSTUT189_L23_LBC_e6e8f83407_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
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<Line id="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0[0]: v" quantity="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0/0/cSTUT189_L23_LBC_e6e8f83407_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
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</Display>
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<OutputFile id="Volts_file__Pop_cSTUT189_L23_LBC_e6e8f83407_0_0" fileName="L23_LBC_cSTUT189_1.Pop_cSTUT189_L23_LBC_e6e8f83407_0_0.v.dat">
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<OutputColumn id="v_Pop_cSTUT189_L23_LBC_e6e8f83407_0_0_0_cSTUT189_L23_LBC_e6e8f83407_0_0_v" quantity="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0/0/cSTUT189_L23_LBC_e6e8f83407_0_0/v"/>
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<OutputColumn id="v_Pop_cSTUT189_L23_LBC_e6e8f83407_0_0_0_cSTUT189_L23_LBC_e6e8f83407_0_0_v" quantity="Pop_cSTUT189_L23_LBC_e6e8f83407_0_0/0/cSTUT189_L23_LBC_e6e8f83407_0_0/v"/>
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</OutputFile>
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</Simulation>
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</Lems>

‎NMC/NeuroML2/LEMS_L23_NBC_cNAC187_1.xml‎

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<Lems>
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<!--
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This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
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This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
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-->
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<!-- Specify which component to run -->
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<Target component="L23_NBC_cNAC187_1" reportFile="report.l23ncb.__SIMULATOR__.txt"/>
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<Target component="L23_NBC_cNAC187_1" reportFile="report.L23_NBC.__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="cNAC187_L23_NBC_9d37c4b1f8.stepcurrent3.net.nml"/>
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<Include file="cNAC187_L23_NBC_9d37c4b1f8_0_0.cell.nml"/>
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<Include file="K_Tst.channel.nml"/>
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<Include file="CaDynamics_E2_NML2.nml"/>
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<Include file="Ca_LVAst.channel.nml"/>
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<Include file="Ca.channel.nml"/>
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<Simulation id="L23_NBC_cNAC187_1" length="3000ms" step="0.01ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Simulation id="L23_NBC_cNAC187_1" length="3000.0ms" step="0.01ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Display id="DispPop__Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0" title="Membrane potentials of cells in Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
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<Line id="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0[0]: v" quantity="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0/0/cNAC187_L23_NBC_9d37c4b1f8_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
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</Display>
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<OutputFile id="Volts_file__Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0" fileName="L23_NBC_cNAC187_1.Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0.v.dat">
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<OutputColumn id="v_Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0_0_cNAC187_L23_NBC_9d37c4b1f8_0_0_v" quantity="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0/0/cNAC187_L23_NBC_9d37c4b1f8_0_0/v"/>
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<OutputColumn id="v_Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0_0_cNAC187_L23_NBC_9d37c4b1f8_0_0_v" quantity="Pop_cNAC187_L23_NBC_9d37c4b1f8_0_0/0/cNAC187_L23_NBC_9d37c4b1f8_0_0/v"/>
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</OutputFile>
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</Simulation>
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</Lems>

‎NMC/NeuroML2/LEMS_L23_PC_cADpyr229_1.xml‎

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<Lems>
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<!--
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This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
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This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
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-->
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<!-- Specify which component to run -->
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<Target component="L23_PC_cADpyr229_1" reportFile="report.l23.__SIMULATOR__.txt"/>
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<Target component="L23_PC_cADpyr229_1" reportFile="report.L23_PC.__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="cADpyr229_L23_PC_5ecbf9b163.stepcurrent3.net.nml"/>
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<Include file="cADpyr229_L23_PC_5ecbf9b163_0_0.cell.nml"/>
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<Include file="pas.channel.nml"/>
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<Include file="K_Pst.channel.nml"/>
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<Include file="CaDynamics_E2_NML2.nml"/>
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<Include file="Ca_LVAst.channel.nml"/>
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<Simulation id="L23_PC_cADpyr229_1" length="3000ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Simulation id="L23_PC_cADpyr229_1" length="3000.0ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Display id="DispPop__Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" title="Membrane potentials of cells in Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
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<Line id="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0[0]: v" quantity="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
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</Display>
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<OutputFile id="Volts_file__Pop_cADpyr229_L23_PC_5ecbf9b163_0_0" fileName="L23_PC_cADpyr229_1.Pop_cADpyr229_L23_PC_5ecbf9b163_0_0.v.dat">
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<OutputColumn id="v_Pop_cADpyr229_L23_PC_5ecbf9b163_0_0_0_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v"/>
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<OutputColumn id="v_Pop_cADpyr229_L23_PC_5ecbf9b163_0_0_0_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="Pop_cADpyr229_L23_PC_5ecbf9b163_0_0/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v"/>
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</OutputFile>
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</Simulation>
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</Lems>

‎NMC/NeuroML2/LEMS_L5_TTPC1_cADpyr232_1.xml‎

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<Lems>
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<!--
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This LEMS file has been automatically generated using PyNeuroML v0.7.2 (libNeuroML v0.4.1)
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This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
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-->
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<!-- Specify which component to run -->
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<Target component="L5_TTPC1_cADpyr232_1" reportFile="report.l5.__SIMULATOR__.txt"/>
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<Target component="L5_TTPC1_cADpyr232_1" reportFile="report.L5_TTPC1.__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="cADpyr232_L5_TTPC1_0fb1ca4724.stepcurrent3.net.nml"/>
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<Include file="cADpyr232_L5_TTPC1_0fb1ca4724_0_0.cell.nml"/>
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<Include file="pas.channel.nml"/>
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<Include file="K_Pst.channel.nml"/>
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<Include file="CaDynamics_E2_NML2.nml"/>
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<Include file="Ca_LVAst.channel.nml"/>
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<Simulation id="L5_TTPC1_cADpyr232_1" length="3000ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Simulation id="L5_TTPC1_cADpyr232_1" length="3000.0ms" step="0.025ms" target="network" seed="1234"> <!-- Note seed: ensures same random numbers used every run -->
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<Display id="DispPop__Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0" title="Membrane potentials of cells in Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0" timeScale="1ms" xmin="-300.0" xmax="3300.0000000000005" ymin="-90" ymax="50">
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<Line id="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0[0]: v" quantity="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0/0/cADpyr232_L5_TTPC1_0fb1ca4724_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
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</Display>
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<OutputFile id="Volts_file__Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0" fileName="L5_TTPC1_cADpyr232_1.Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0.v.dat">
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<OutputColumn id="v_Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_0_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_v" quantity="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0/0/cADpyr232_L5_TTPC1_0fb1ca4724_0_0/v"/>
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<OutputColumn id="v_Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_0_cADpyr232_L5_TTPC1_0fb1ca4724_0_0_v" quantity="Pop_cADpyr232_L5_TTPC1_0fb1ca4724_0_0/0/cADpyr232_L5_TTPC1_0fb1ca4724_0_0/v"/>
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</OutputFile>
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</Simulation>
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</Lems>

‎NMC/NeuroML2/bAC217_L4_MC_5fa0a62bd0_0_0.cell.nml‎

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<inhomogeneousValue value="1e4 * ((-0.869600 + 2.087000*exp((p--1000.000000)*-0.003000))*0.000371)" inhomogeneousParameter="PathLengthOver_apical"/>
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</variableParameter>
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</channelDensityNonUniform>
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<spikeThresh value="10mV"/>
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<specificCapacitance segmentGroup="basal" value="1.0 uF_per_cm2"/>
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<specificCapacitance segmentGroup="apical" value="1.0 uF_per_cm2"/>
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<specificCapacitance segmentGroup="axonal" value="1.0 uF_per_cm2"/>

‎NMC/NeuroML2/bNAC219_L1_DAC_a9ae5cbbf5_0_0.cell.nml‎

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<inhomogeneousValue value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003000))*0.000049)" inhomogeneousParameter="PathLengthOver_apical"/>
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</variableParameter>
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</channelDensityNonUniform>
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<spikeThresh value="10mV"/>
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<specificCapacitance segmentGroup="basal" value="1.0 uF_per_cm2"/>
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<specificCapacitance segmentGroup="apical" value="1.0 uF_per_cm2"/>
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<specificCapacitance segmentGroup="axonal" value="1.0 uF_per_cm2"/>

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