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Merge pull request #185 from NeuroML/development
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Regenerated files & updates to single Izh notebook example
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@pgleeson
pgleeson authored Dec 15, 2023
2 parents 72979f7 + c5483dc commit 495897d
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28 changes: 28 additions & 0 deletions .gitignore
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/source/Userdocs/NML2_examples/LEMS_Test_SKv3_1.xml
/source/Userdocs/NML2_examples/LEMS_iv_complex_cell.xml
arm64
/source/Userdocs/NML2_examples/Ca.channel.nml
/source/Userdocs/NML2_examples/CaDynamics_E2_NML2.nml
/source/Userdocs/NML2_examples/Ca_LVAst.channel.nml
/source/Userdocs/NML2_examples/Exc.spikes
/source/Userdocs/NML2_examples/Ih.channel.nml
/source/Userdocs/NML2_examples/Im.channel.nml
/source/Userdocs/NML2_examples/Inh.spikes
/source/Userdocs/NML2_examples/K_Pst.channel.nml
/source/Userdocs/NML2_examples/K_Tst.channel.nml
/source/Userdocs/NML2_examples/LEMS_NML_DB_network_sim.xml
/source/Userdocs/NML2_examples/LEMS_iv_bAC217_L23_MC_40be3bf0e8_0_0.xml
/source/Userdocs/NML2_examples/LEMS_iv_novel_cell.xml
/source/Userdocs/NML2_examples/NMLCH000015.channel.nml
/source/Userdocs/NML2_examples/NMLCL000109.nml.zip
/source/Userdocs/NML2_examples/NML_DB_Net.gv.png
/source/Userdocs/NML2_examples/NML_DB_network.net.nml
/source/Userdocs/NML2_examples/NaTa_t.channel.nml
/source/Userdocs/NML2_examples/NaTs2_t.channel.nml
/source/Userdocs/NML2_examples/Nap_Et2.channel.nml
/source/Userdocs/NML2_examples/SK_E2.channel.nml
/source/Userdocs/NML2_examples/SKv3_1.channel.nml
/source/Userdocs/NML2_examples/TestCell.cell.nml
/source/Userdocs/NML2_examples/bAC217_L23_MC_40be3bf0e8_0_0.cell.nml
/source/Userdocs/NML2_examples/bAC217_L23_MC_40be3bf0e8_0_0.hoc
/source/Userdocs/NML2_examples/iv_bAC217_L23_MC_40be3bf0e8_0_0.net.nml
/source/Userdocs/NML2_examples/iv_novel_cell.net.nml
/source/Userdocs/NML2_examples/novel_cell.hoc
/source/Userdocs/NML2_examples/pas.channel.nml
2 changes: 1 addition & 1 deletion source/Userdocs/NML2_examples/HH_example_k_channel.nml
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<notes>k channel for HH neuron</notes>
<ionChannelHH id="k_channel" species="k" conductance="10pS">
<notes>Potassium channel for HH cell</notes>
<gateHHrates id="k_n" instances="4">
<gateHHrates id="n" instances="4">
<notes>n gate for k channel</notes>
<forwardRate type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
<reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
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21 changes: 10 additions & 11 deletions source/Userdocs/NML2_examples/LEMS_HH_single_compartment_example_sim.xml
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<Lems>

<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
This LEMS file has been automatically generated using PyNeuroML v1.1.10 (libNeuroML v0.5.8)
-->

<!-- Specify which component to run -->
<Target component="HH_single_compartment_example_sim"/>

<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>

<Include file="HH_example_net.nml"/>
<Include file="HH_example_cell.nml"/>
<Include file="HH_example_na_channel.nml"/>
<Include file="HH_example_k_channel.nml"/>
<Include file="HH_example_leak_channel.nml"/>

<Simulation id="HH_single_compartment_example_sim" length="300ms" step="0.01ms" target="single_hh_cell_network" seed="123"> <!-- Note seed: ensures same random numbers used every run -->

<OutputFile id="output0" fileName="HH_single_compartment_example_sim.dat">
<OutputColumn id="pop0[0]/v" quantity="pop0[0]/v"/>
<OutputColumn id="pop0[0]/iChannels" quantity="pop0[0]/iChannels"/>
<OutputColumn id="pop0[0]/na/iDensity" quantity="pop0[0]/hh_b_prop/membraneProperties/na_channels/iDensity/"/>
<OutputColumn id="pop0[0]/k/iDensity" quantity="pop0[0]/hh_b_prop/membraneProperties/k_channels/iDensity/"/>
<OutputColumn id="pop0[0]/v" quantity="pop0[0]/v"/>
<OutputColumn id="pop0[0]/iChannels" quantity="pop0[0]/iChannels"/>
<OutputColumn id="pop0[0]/na/iDensity" quantity="pop0[0]/hh_b_prop/membraneProperties/na_channels/iDensity/"/>
<OutputColumn id="pop0[0]/k/iDensity" quantity="pop0[0]/hh_b_prop/membraneProperties/k_channels/iDensity/"/>
</OutputFile>

</Simulation>

</Lems>
15 changes: 7 additions & 8 deletions source/Userdocs/NML2_examples/LEMS_example-single-izhikevich2007cell-sim.xml
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<Lems>

<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
This LEMS file has been automatically generated using PyNeuroML v1.1.10 (libNeuroML v0.5.8)
-->

<!-- Specify which component to run -->
<Target component="example-single-izhikevich2007cell-sim"/>

<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>

<Include file="izhikevich2007_single_cell_network.nml"/>

<Simulation id="example-single-izhikevich2007cell-sim" length="1000ms" step="0.1ms" target="IzNet" seed="123"> <!-- Note seed: ensures same random numbers used every run -->

<OutputFile id="output0" fileName="example-single-izhikevich2007cell-sim.v.dat">
<OutputColumn id="IzhPop0[0]" quantity="IzhPop0[0]/v"/>
<OutputColumn id="IzhPop0[0]" quantity="IzhPop0[0]/v"/>
</OutputFile>

</Simulation>

</Lems>
35 changes: 17 additions & 18 deletions source/Userdocs/NML2_examples/LEMS_example_izhikevich2007network_sim.xml
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<Lems>

<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
This LEMS file has been automatically generated using PyNeuroML v1.1.10 (libNeuroML v0.5.8)
-->

<!-- Specify which component to run -->
<Target component="example_izhikevich2007network_sim"/>

<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>

<Include file="izhikevich2007_network.nml"/>

<Simulation id="example_izhikevich2007network_sim" length="1000ms" step="0.1ms" target="IzNet" seed="123"> <!-- Note seed: ensures same random numbers used every run -->

<EventOutputFile id="pop0" fileName="example_izhikevich2007network_sim.0.spikes.dat" format="ID_TIME">
<EventSelection id="0" select="IzPop0[0]" eventPort="spike"/>
<EventSelection id="1" select="IzPop0[1]" eventPort="spike"/>
<EventSelection id="2" select="IzPop0[2]" eventPort="spike"/>
<EventSelection id="3" select="IzPop0[3]" eventPort="spike"/>
<EventSelection id="4" select="IzPop0[4]" eventPort="spike"/>
<EventSelection id="0" select="IzPop0[0]" eventPort="spike"/>
<EventSelection id="1" select="IzPop0[1]" eventPort="spike"/>
<EventSelection id="2" select="IzPop0[2]" eventPort="spike"/>
<EventSelection id="3" select="IzPop0[3]" eventPort="spike"/>
<EventSelection id="4" select="IzPop0[4]" eventPort="spike"/>
</EventOutputFile>

<EventOutputFile id="pop1" fileName="example_izhikevich2007network_sim.1.spikes.dat" format="ID_TIME">
<EventSelection id="0" select="IzPop1[0]" eventPort="spike"/>
<EventSelection id="1" select="IzPop1[1]" eventPort="spike"/>
<EventSelection id="2" select="IzPop1[2]" eventPort="spike"/>
<EventSelection id="3" select="IzPop1[3]" eventPort="spike"/>
<EventSelection id="4" select="IzPop1[4]" eventPort="spike"/>
<EventSelection id="0" select="IzPop1[0]" eventPort="spike"/>
<EventSelection id="1" select="IzPop1[1]" eventPort="spike"/>
<EventSelection id="2" select="IzPop1[2]" eventPort="spike"/>
<EventSelection id="3" select="IzPop1[3]" eventPort="spike"/>
<EventSelection id="4" select="IzPop1[4]" eventPort="spike"/>
</EventOutputFile>

</Simulation>

</Lems>
31 changes: 15 additions & 16 deletions source/Userdocs/NML2_examples/LEMS_olm_example_sim.xml
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<Lems>

<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
This LEMS file has been automatically generated using PyNeuroML v1.1.10 (libNeuroML v0.5.8)
-->

<!-- Specify which component to run -->
<Target component="olm_example_sim"/>

<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>

<Include file="olm_example_net.nml"/>
<Include file="olm.cell.nml"/>
<Include file="olm-example/leak_chan.channel.nml"/>
<Include file="olm-example/HCNolm.channel.nml"/>
<Include file="olm-example/Kdrfast.channel.nml"/>
<Include file="olm-example/KvAolm.channel.nml"/>
<Include file="olm-example/Nav.channel.nml"/>

<Simulation id="olm_example_sim" length="600ms" step="0.01ms" target="single_olm_cell_network" seed="123"> <!-- Note seed: ensures same random numbers used every run -->

<OutputFile id="output0" fileName="olm_example_sim.dat">
<OutputColumn id="pop0_0_v" quantity="pop0[0]/v"/>
<OutputColumn id="pop0_0_v_Seg0_soma_0" quantity="pop0/0/olm/0/v"/>
<OutputColumn id="pop0_0_v_Seg1_soma_0" quantity="pop0/0/olm/1/v"/>
<OutputColumn id="pop0_0_v_Seg0_axon_0" quantity="pop0/0/olm/2/v"/>
<OutputColumn id="pop0_0_v_Seg1_axon_0" quantity="pop0/0/olm/3/v"/>
<OutputColumn id="pop0_0_v_Seg0_dend_0" quantity="pop0/0/olm/4/v"/>
<OutputColumn id="pop0_0_v_Seg1_dend_0" quantity="pop0/0/olm/6/v"/>
<OutputColumn id="pop0_0_v_Seg0_dend_1" quantity="pop0/0/olm/5/v"/>
<OutputColumn id="pop0_0_v_Seg1_dend_1" quantity="pop0/0/olm/7/v"/>
<OutputColumn id="pop0_0_v" quantity="pop0[0]/v"/>
<OutputColumn id="pop0_0_v_Seg0_soma_0" quantity="pop0/0/olm/0/v"/>
<OutputColumn id="pop0_0_v_Seg1_soma_0" quantity="pop0/0/olm/1/v"/>
<OutputColumn id="pop0_0_v_Seg0_axon_0" quantity="pop0/0/olm/2/v"/>
<OutputColumn id="pop0_0_v_Seg1_axon_0" quantity="pop0/0/olm/3/v"/>
<OutputColumn id="pop0_0_v_Seg0_dend_0" quantity="pop0/0/olm/4/v"/>
<OutputColumn id="pop0_0_v_Seg1_dend_0" quantity="pop0/0/olm/6/v"/>
<OutputColumn id="pop0_0_v_Seg0_dend_1" quantity="pop0/0/olm/5/v"/>
<OutputColumn id="pop0_0_v_Seg1_dend_1" quantity="pop0/0/olm/7/v"/>
</OutputFile>

</Simulation>

</Lems>
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