/
simple_cell.cell.nml
132 lines (85 loc) · 6.02 KB
/
simple_cell.cell.nml
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<?xml version="1.0" encoding="UTF-8"?>
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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_Golgi">
<!-- Example of a multicompartmental cell with biophysics in NeuroML 2 -->
<!-- This is a "pure" NeuroML 2 file. It cannot currently used for simulations with
jLEMS/jNeuroML however, as jLEMS does not yet support multicompartmental cells -->
<include href="Golgi_Na.channel.nml"/>
<include href="Golgi_NaR.channel.nml"/>
<include href="Golgi_NaP.channel.nml"/>
<include href="Golgi_KA.channel.nml"/>
<!--include href="Golgi_SK2.channel.nml"/-->
<include href="Golgi_KM.channel.nml"/>
<include href="Golgi_KV.channel.nml"/>
<include href="Golgi_BK.channel.nml"/>
<include href="Golgi_CaHVA.channel.nml"/>
<include href="Golgi_CaLVA.channel.nml"/>
<include href="Golgi_HCN1f.channel.nml"/>
<include href="Golgi_HCN1s.channel.nml"/>
<include href="Golgi_HCN2f.channel.nml"/>
<include href="Golgi_HCN2s.channel.nml"/>
<include href="Golgi_lkg.channel.nml"/>
<include href="Golgi_CALC.nml"/>
<include href="Golgi_CALC2.nml"/>
<!-- Note, no <cells> element... -->
<cell id="GoCl" >
<notes>A Single Compartment Cerebellar Golgi cell for testing</notes>
<!-- Suggestion for annotation scheme based on reference to MIRIAM resource -->
<morphology id="simpleGoC">
<segment id ="0" name="Soma">
<!-- no parent => root segment -->
<proximal x="0" y="0" z="0" diameter="27"/>
<distal x="27" y="0" z="0" diameter="27"/>
</segment>
<!-- segmentGroups follow -->
<segmentGroup id="Soma" neuroLexId="sao864921383"> <!--
This group contains an unbranched set of segments, and all of the segmentGroups marked with
neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
These segmentGroups correspond to the 'cables' of NeuroML v1.8.1. -->
<member segment="0"/>
</segmentGroup>
<segmentGroup id="soma_group" neuroLexId="GO:0043025"> <!--Soma group-->
<include segmentGroup="Soma"/>
</segmentGroup>
</morphology>
<biophysicalProperties id="bio_GoC">
<membraneProperties>
<!--Leak -->
<channelDensity condDensity="0.021 mS_per_cm2" id="Leak" ionChannel="LeakConductance" erev="-55.0 mV" ion="non_specific"/>
<!-- Na channels -->
<channelDensity condDensity="48.0 mS_per_cm2" id="Golgi_Na_soma_group" ionChannel="GolgiNa" segmentGroup="soma_group" ion="na" erev="87.39 mV"/>
<channelDensity condDensity="0.19 mS_per_cm2" id="Golgi_NaP_soma_group" ionChannel="GolgiNaP" segmentGroup="soma_group" ion="na" erev="87.39 mV"/>
<channelDensity condDensity="1.7 mS_per_cm2" id="Golgi_NaR_soma_group" ionChannel="GolgiNaR" segmentGroup="soma_group" ion="na" erev="87.39 mV"/>
<!--Potassium channels-->
<channelDensity condDensity="8.0 mS_per_cm2" id="Golgi_KA_soma_group" ionChannel="GolgiKA" segmentGroup="soma_group" ion="k" erev="-84.69 mV"/>
<channelDensity condDensity="32.0 mS_per_cm2" id="Golgi_KV_soma_group" ionChannel="GolgiKV" segmentGroup="soma_group" ion="k" erev="-84.69 mV"/>
<channelDensity condDensity="1.0 mS_per_cm2" id="Golgi_KM_soma_group" ionChannel="GolgiKM" segmentGroup="soma_group" ion="k" erev="-84.69 mV"/>
<!--Ca-dep K+ channels-->
<channelDensity condDensity="3.0 mS_per_cm2" id="Golgi_BK_soma_group" ionChannel="GolgiBK" segmentGroup="soma_group" ion="k" erev="-84.69 mV"/>
<!--ChannelDensity condDensity="38.0 mS_per_cm2" id="Golgi_KAHP_soma_group" ionChannel="GolgiSK2" segmentGroup="soma_group" ion="k" erev="-84.69 mV"/-->
<!--HCN channels-->
<channelDensity condDensity="0.05 mS_per_cm2" id="Golgi_hcn1f_soma_group" ionChannel="GolgiHCN1f" segmentGroup="soma_group" ion="h" erev="-20.0 mV"/>
<channelDensity condDensity="0.05 mS_per_cm2" id="Golgi_hcn1s_soma_group" ionChannel="GolgiHCN1s" segmentGroup="soma_group" ion="h" erev="-20.0 mV"/>
<channelDensity condDensity="0.08 mS_per_cm2" id="Golgi_hcn2f_soma_group" ionChannel="GolgiHCN2f" segmentGroup="soma_group" ion="h" erev="-20.0 mV"/>
<channelDensity condDensity="0.08 mS_per_cm2" id="Golgi_hcn2s_soma_group" ionChannel="GolgiHCN2s" segmentGroup="soma_group" ion="h" erev="-20.0 mV"/>
<!--calcium channnels -->
<channelDensityNernst condDensity="0.46 mS_per_cm2" id="Golgi_Ca_HVA_soma_group" ionChannel="GolgiCaHVA" segmentGroup="soma_group" ion="ca"/> <!--calculate erev by nernst eqn-->
<channelDensityNernst condDensity="0.25 mS_per_cm2" id="Ca_LVA_soma_group" ionChannel="GolgiCaLVA" segmentGroup="soma_group" ion="ca2"/>
<!-- general properties-->
<spikeThresh value="0.0 mV"/>
<specificCapacitance value="1.0 uF_per_cm2"/>
<initMembPotential value="-60.0 mV"/>
</membraneProperties>
<intracellularProperties>
<resistivity value="0.1 kohm_cm"/> <!-- Used for specific axial resistance, not nec for single segment model that is isolpotential -->
<species segmentGroup="soma_group" id="ca" ion="ca" concentrationModel="Golgi_CALC" initialConcentration="5e-5mM" initialExtConcentration="2mM"/>
<species segmentGroup="soma_group" id="ca2" ion="ca2" concentrationModel="Golgi_CALC2" initialConcentration="5e-5mM" initialExtConcentration="2mM"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
<network id="net1" type="networkWithTemperature" temperature="23 degC">
<population id="gocpop" component="GoCl" size="1"/>
</network>
</neuroml>