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Merge pull request #7 from sanjayankur31/neuroml-ankur
Complete conversion of KC cell
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,12 @@ | ||
| *.dat | ||
| x86_64/ | ||
| channels/*dat | ||
| NeuroML2/channels/LEMS* | ||
| NeuroML2/channels/*mod | ||
| NeuroML2/*mod | ||
| NeuroML2/*.hoc | ||
| NeuroML2/*.dat | ||
| NeuroML2/*_nrn.py | ||
| NeuroML2/*.spikes | ||
| .mypy_cache/ | ||
| *.npy |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| #!/bin/bash | ||
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| # Copyright 2024 Ankur Sinha | ||
| # Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com> | ||
| # File : | ||
| # | ||
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| if [[ -z "${MODEL_DIR}" ]]; then | ||
| export MODEL_DIR=$(pwd) | ||
| echo "Setting model root directory to $MODEL_DIR" | ||
| echo "To use a custom path, set the MODEL_DIR environment variable to the desired path." | ||
| fi | ||
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| export PYTHONPATH="${MODEL_DIR}/mb:${MODEL_DIR}/nrn:${MODEL_DIR}/morphutils:${MODEL_DIR}/common" | ||
| nrnivmodl ./mb/mod/ | ||
| python ./mb/test_cell/test_kc.py |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| target: LEMS_KC_step_test.xml | ||
| engine: jNeuroML_NEURON | ||
| mep: .test.kc.mep | ||
| experiments: | ||
| stepKC: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: KC_step_test.KC_pop.v.dat | ||
| columns: [0,1] | ||
| scaling: [1000,1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -10. | ||
| tolerance: 0.005087969567027844 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| system: Testing a detailed cell | ||
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| experiments: | ||
| stepKC: | ||
| expected: | ||
| spike times: [144.45000000000556, 177.64999999997536, 210.29999999994567, 242.74999999991616, 275.0499999998868, 307.19999999985754, 339.2249999998284, 371.07499999979945, 402.74999999977064, 434.1499999997421, 465.2249999997138, 495.87499999968594, 525.9749999997221, 555.3499999998289, 583.8499999999326] | ||
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| # generated from test-kc.py |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| <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.xsd" id="KC_doc"> | ||
| <include href="channels/pas.channel.nml"/> | ||
| <include href="channels/kv.channel.nml"/> | ||
| <include href="channels/ka.channel.nml"/> | ||
| <include href="channels/kst.channel.nml"/> | ||
| <include href="channels/naf.channel.nml"/> | ||
| <include href="channels/nas.channel.nml"/> | ||
| <cell id="KC"> | ||
| <morphology id="morphology"> | ||
| <segment id="0" name="Seg0"> | ||
| <proximal x="0.0" y="0.0" z="0.0" diameter="20.0"/> | ||
| <distal x="0.0" y="0.0" z="6.366" diameter="20.0"/> | ||
| </segment> | ||
| <segmentGroup id="soma_group" neuroLexId="GO:0043025"> | ||
| <notes>Default soma segment group for the cell</notes> | ||
| <member segment="0"/> | ||
| </segmentGroup> | ||
| <segmentGroup id="all"> | ||
| <notes>Default segment group for all segments in the cell</notes> | ||
| <member segment="0"/> | ||
| </segmentGroup> | ||
| </morphology> | ||
| <biophysicalProperties id="biophys"> | ||
| <membraneProperties> | ||
| <channelDensity id="pas" ionChannel="pas" condDensity="9.75e-5 S_per_cm2" erev="-70 mV" ion="non_specific"/> | ||
| <channelDensity id="kv" ionChannel="kv" condDensity="1.5e-3 S_per_cm2" erev="-81 mV" ion="k"/> | ||
| <channelDensity id="ka" ionChannel="ka" condDensity="1.4525e-2 S_per_cm2" erev="-81 mV" ion="k"/> | ||
| <channelDensity id="kst" ionChannel="kst" condDensity="2.0275e-3 S_per_cm2" erev="-81 mV" ion="k"/> | ||
| <channelDensity id="naf" ionChannel="naf" condDensity="3.5e-2 S_per_cm2" erev="58 mV" ion="na"/> | ||
| <channelDensity id="nas" ionChannel="nas" condDensity="3e-3 S_per_cm2" erev="58 mV" ion="na"/> | ||
| <spikeThresh value="-10mV"/> | ||
| <specificCapacitance value="1 uF_per_cm2"/> | ||
| <initMembPotential value="-70mV"/> | ||
| </membraneProperties> | ||
| <intracellularProperties> | ||
| <resistivity value="35.4 ohm_cm"/> | ||
| </intracellularProperties> | ||
| </biophysicalProperties> | ||
| </cell> | ||
| <pulseGenerator id="pg" delay="100ms" duration="500ms" amplitude="16pA"/> | ||
| <network id="KC_net"> | ||
| <population id="KC_pop" component="KC" size="1"/> | ||
| <inputList id="input_list" population="KC_pop" component="pg"> | ||
| <input id="0" target="../KC_pop[0]" destination="synapses" segmentId="0"/> | ||
| </inputList> | ||
| </network> | ||
| </neuroml> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| <Lems> | ||
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| <!-- | ||
| This LEMS file has been automatically generated using PyNeuroML v1.2.8 (libNeuroML v0.5.9) | ||
| --> | ||
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| <!-- Specify which component to run --> | ||
| <Target component="KC_step_test"/> | ||
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| <!-- Include core NeuroML2 ComponentType definitions --> | ||
| <Include file="Cells.xml"/> | ||
| <Include file="Networks.xml"/> | ||
| <Include file="Simulation.xml"/> | ||
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| <Include file="KC.net.nml"/> | ||
| <Include file="channels/pas.channel.nml"/> | ||
| <Include file="channels/kv.channel.nml"/> | ||
| <Include file="RaySigmoid.nml"/> | ||
| <Include file="channels/ka.channel.nml"/> | ||
| <Include file="channels/kst.channel.nml"/> | ||
| <Include file="channels/naf.channel.nml"/> | ||
| <Include file="channels/nas.channel.nml"/> | ||
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| <Simulation id="KC_step_test" length="700.0ms" step="0.01ms" target="KC_net" seed="12345"> <!-- Note seed: ensures same random numbers used every run --> | ||
| <Display id="DispPop__KC_pop" title="Membrane potentials of cells in KC_pop" timeScale="1ms" xmin="-70.0" xmax="770.0000000000001" ymin="-90" ymax="50"> | ||
| <Line id="KC_pop[0]: v" quantity="KC_pop[0]/v" scale="1mV" color="#d54f33" timeScale="1ms"/> | ||
| </Display> | ||
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| <OutputFile id="Volts_file__KC_pop" fileName="KC_step_test.KC_pop.v.dat"> | ||
| <OutputColumn id="v_KC_pop_0__v" quantity="KC_pop[0]/v"/> | ||
| </OutputFile> | ||
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| <OutputFile id="k_dat" fileName="k.dat"> | ||
| <OutputColumn id="KC_pop_0__biophys_membraneProperties_kv_iDensity" quantity="KC_pop[0]/biophys/membraneProperties/kv/iDensity"/> | ||
| </OutputFile> | ||
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| <EventOutputFile id="Spikes_file__KC_pop" fileName="KC_step_test.KC_pop.spikes" format="ID_TIME"> | ||
| <EventSelection id="0" select="KC_pop[0]" eventPort="spike"/> | ||
| </EventOutputFile> | ||
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| </Simulation> | ||
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| </Lems> |
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