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Merge pull request #2 from OpenSourceBrain/development
Test on linux & mac 14
2 parents a0a47e7 + d0f33bd commit 281de79

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‎.github/workflows/omv-ci.yml

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on:
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push:
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branches: [ main, development ]
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branches: [ main, development, experimental ]
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pull_request:
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branches: [ main, development ]
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branches: [ main, development, experimental ]
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jobs:
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build:
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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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runs-on: [ ubuntu-latest, macos-latest, macos-11 ]
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engine: [ jNeuroML, jNeuroML_NEURON, jNeuroML_EDEN, jNeuroML_validate, EDEN, "EDEN:0.2.0" ]
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runs-on: [ ubuntu-latest, macos-14 ]
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engine:
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- jNeuroML
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- jNeuroML_NEURON
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- jNeuroML_EDEN
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- "jNeuroML_EDEN:0.2.3"
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- jNeuroML_validate
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- "EDEN:0.2.0"
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- "EDEN:0.2.2"
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- "EDEN:0.2.3"
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python-version: [ "3.10" ]
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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/pip-install.yml

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runs-on: [ubuntu-latest, macos-latest, windows-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@v3
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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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‎.gitignore

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x86_64
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*_nrn.py
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arm64
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/NeuroML2/hhcell.hoc
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/NeuroML2/report.*.txt

‎NeuroML2/.test.2007.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: 0.000
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tolerance: 3.667537832120739e-08 # due to slight difference on mac/linux of eden...

‎NeuroML2/.test.eden.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
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tolerance: 3.667537832120739e-08 # due to slight difference on mac/linux of eden...

‎NeuroML2/.test.ex5.eden.omt

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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target: LEMS_NML2_Ex5_DetCell.xml
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engine: jNeuroML_EDEN
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mep: .test.ex5.mep
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experiments:
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v:
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observables:
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spike times:
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file:
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path: ex5_v.dat
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columns: [0,1]
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scaling: [1000, 1000]
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spike detection:
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method: threshold
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threshold: 0
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tolerance: 0.0035033174501254887
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m:
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observables:
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spike times:
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file:
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path: ex5_vars.dat
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columns: [0,1]
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scaling: [1000, 1]
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spike detection:
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method: threshold
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threshold: 0.9
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tolerance: 0.0035249957767891716

‎NeuroML2/.test.ex5.jnml.omt

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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target: LEMS_NML2_Ex5_DetCell.xml
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engine: jNeuroML
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mep: .test.ex5.mep
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experiments:
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v:
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observables:
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spike times:
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file:
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path: ex5_v.dat
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columns: [0,1]
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scaling: [1000, 1000]
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spike detection:
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method: threshold
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threshold: 0
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tolerance: 0.005542225676726113
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m:
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observables:
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spike times:
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file:
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path: ex5_vars.dat
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columns: [0,1]
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scaling: [1000, 1]
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spike detection:
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method: threshold
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threshold: 0.9
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tolerance: 0.005574638211610937

‎NeuroML2/.test.ex5.jnmlnrn.omt

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# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
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target: LEMS_NML2_Ex5_DetCell.xml
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engine: jNeuroML_NEURON
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mep: .test.ex5.mep
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experiments:
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v:
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observables:
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spike times:
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file:
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path: ex5_v.dat
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columns: [0,1]
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scaling: [1000, 1000]
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spike detection:
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method: threshold
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threshold: 0
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tolerance: 0
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m:
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observables:
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spike times:
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file:
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path: ex5_vars.dat
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columns: [0,1]
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scaling: [1000, 1]
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spike detection:
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method: threshold
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threshold: 0.9
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tolerance: 0

‎NeuroML2/.test.ex5.mep

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system: Test Ex0
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experiments:
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v:
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expected:
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spike times: [102.22, 118.46, 134.5, 150.51999999999998, 166.55, 182.57999999999998, 198.6, 214.63, 230.65, 246.68, 262.71, 278.72999999999996, 294.76000000000005, 310.79, 326.81, 342.84, 358.86, 374.89, 390.92, 406.94, 422.97, 439.0, 455.02, 471.05, 487.07, 503.09999999999997, 519.13, 535.15, 551.18, 567.2, 583.23, 599.26, 615.2800000000001, 631.3100000000001, 647.34, 663.3599999999999, 679.3900000000001, 695.41, 711.4399999999999, 727.4699999999999, 743.49, 759.52, 775.55, 791.57, 807.6, 823.62, 839.65, 855.68, 871.7, 887.73]
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m:
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expected:
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spike times: [102.44, 118.69, 134.72, 150.75, 166.77, 182.79999999999998, 198.83, 214.85000000000002, 230.88, 246.9, 262.93, 278.96, 294.98, 311.01, 327.04, 343.06, 359.09000000000003, 375.11, 391.14, 407.16999999999996, 423.19, 439.22, 455.25, 471.27000000000004, 487.3, 503.32, 519.35, 535.38, 551.4, 567.43, 583.45, 599.48, 615.51, 631.5300000000001, 647.5600000000001, 663.59, 679.61, 695.64, 711.66, 727.6899999999999, 743.72, 759.74, 775.77, 791.8, 807.8199999999999, 823.85, 839.87, 855.9, 871.93, 887.95]

‎NeuroML2/LEMS_NML2_Ex5_DetCell.xml

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<Lems>
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<!-- Example with Simple cell specifying segment details-->
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<!-- This is a file which can be read and executed by the LEMS Interpreter.
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It imports the LEMS definitions of the core NeuroML 2 Components,
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imports in "pure" NeuroML 2 and contains some LEMS elements for running
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a simulation -->
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<Target component="sim1" reportFile="report.ex5.txt"/>
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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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<!-- Including file with a <neuroml> root, a "real" NeuroML 2 file -->
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<Include file="NML2_SingleCompHHCell.nml"/>
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<Simulation id="sim1" length="1000ms" step="0.01ms" target="net1">
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<Display id="d1" title="Ex5: HH cell with simple morphology: voltage" timeScale="1ms" xmin="0" xmax="300" ymin="-90" ymax="50">
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<Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#cccccc" timeScale="1ms"/>
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<Line id="spiking" quantity="hhpop[0]/spiking" scale="0.1V" color="#004040" timeScale="1ms"/>
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<!--<Line id="l3" quantity="hhpop[0]/debugVal" scale="1V" color="#999999" timeScale="1ms"/>-->
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</Display>
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<Display id="d2" title="Ex5: HH cell with simple morphology: rate variables" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1">
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<Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1" color="#000000" timeScale="1ms"/>
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<Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1" color="#ff0000" timeScale="1ms"/>
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<Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1" color="#0000ff" timeScale="1ms"/>
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</Display>
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<Display id="d3" title="Ex5: HH cell with simple morphology: current densities" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1">
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<Line id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1" color="#000000" timeScale="1ms"/>
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<Line id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1" color="#ff0000" timeScale="1ms"/>
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</Display>
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<Display id="d4" title="Ex5: HH cell with simple morphology: conductance densities" timeScale="1ms" xmin="0" xmax="300" ymin="-50" ymax="350">
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<Line id="gna" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/gDensity" scale="1" color="#000000" timeScale="1ms"/>
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<Line id="gk" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/gDensity" scale="1" color="#ff0000" timeScale="1ms"/>
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</Display>
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<OutputFile id="of0" fileName="ex5_v.dat">
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<OutputColumn id="v" quantity="hhpop[0]/v"/>
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</OutputFile>
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<OutputFile id="of1" fileName="ex5_vars.dat">
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<OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/>
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<OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/>
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<OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/>
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</OutputFile>
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<!-- Not supported by EDEN...
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<OutputFile id="of2" fileName="results/ex5_curr_dens.dat">
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<OutputColumn id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/>
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<OutputColumn id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity"/>
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</OutputFile>-->
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</Simulation>
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</Lems>

‎NeuroML2/NML2_SingleCompHHCell.nml

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<?xml version="1.0" encoding="UTF-8"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
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id="NML2_SingleCompHHCell">
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<!-- Single compartment cell with HH channels -->
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<!-- This is a "pure" NeuroML 2 file. It can be included in a LEMS file for use in a simulaton
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by the LEMS interpreter, see LEMS_NML2_Ex5_DetCell.xml -->
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<ionChannelHH id="passiveChan" conductance="10pS">
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<notes>Leak conductance</notes>
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</ionChannelHH>
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<ionChannelHH id="naChan" conductance="10pS" species="na">
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<notes>Na channel</notes>
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<gateHHrates id="m" instances="3">
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<forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>
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<reverseRate type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
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</gateHHrates>
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<gateHHrates id="h" instances="1">
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<forwardRate type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>
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<reverseRate type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
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</gateHHrates>
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</ionChannelHH>
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<ionChannelHH id="kChan" conductance="10pS" species="k">
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<gateHHrates id="n" instances="4">
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<forwardRate type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
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<reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
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</gateHHrates>
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</ionChannelHH>
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<cell id="hhcell">
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<morphology id="morph1">
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<segment id="0" name="soma">
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<proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 um^2-->
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<distal x="0" y="0" z="0" diameter="17.841242"/>
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</segment>
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<segmentGroup id="soma_group">
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<member segment="0"/>
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</segmentGroup>
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</morphology>
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<biophysicalProperties id="bioPhys1">
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<membraneProperties>
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<channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0 S_per_m2" erev="-54.3mV" ion="non_specific"/>
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<channelDensity id="naChans" ionChannel="naChan" condDensity="120.0 mS_per_cm2" erev="50.0 mV" ion="na"/>
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<channelDensity id="kChans" ionChannel="kChan" condDensity="360 S_per_m2" erev="-77mV" ion="k"/>
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<spikeThresh value="-20mV"/>
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<specificCapacitance value="1.0 uF_per_cm2"/>
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<initMembPotential value="-65mV"/>
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</membraneProperties>
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<intracellularProperties>
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<resistivity value="0.03 kohm_cm"/> <!-- Note: not used in single compartment simulations -->
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</intracellularProperties>
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</biophysicalProperties>
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</cell>
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<pulseGenerator id="pulseGen1" delay="100ms" duration="800ms" amplitude="0.08nA"/>
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<network id="net1">
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<population id="hhpop" component="hhcell" size="1"/>
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<explicitInput target="hhpop[0]" input="pulseGen1"/>
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</network>
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</neuroml>
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‎NeuroML2/clean.sh

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rm x86_64 *.c *.so *.dat
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rm -rf x86_64 arm64
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mv *nrn.py LEMS*_eden.py *.c *.so *.dat *.mod *txt *.hoc /tmp

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