Permalink
Fetching contributors…
Cannot retrieve contributors at this time
110 lines (74 sloc) 4.2 KB
<?xml version="1.0" encoding="UTF-8"?>
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xi="http://www.w3.org/2001/XInclude"
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
id="NML2_FullCell">
<!-- 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="NML2_SimpleIonChannel.nml"/> <!-- Contains ionChannel NaConductance -->
<ionChannelHH id="pas" conductance="10pS"/> <!--For use in example cell below-->
<!-- Note, no <cells> element... -->
<cell id="SpikingCell" metaid="HippoCA1Cell">
<notes>A Simple Spiking cell for testing purposes</notes>
<!-- Suggestion for annotation scheme based on reference to MIRIAM resource -->
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="HippoCA1Cell">
<bqbiol:is>
<rdf:Bag>
<!-- This cell model is a version of a hippocampal CA1 pyramidal cell -->
<rdf:li rdf:resource="urn:miriam:neurondb:258"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
<morphology id="SpikingCell_morphology">
<segment id ="0" name="Soma">
<!-- no parent => root segment -->
<proximal x="0" y="0" z="0" diameter="10"/>
<distal x="10" y="0" z="0" diameter="10"/>
</segment>
<segment id ="1" name="Dendrite1">
<parent segment="0"/>
<!-- no proximal => use distal of parent -->
<distal x="20" y="0" z="0" diameter="3"/>
</segment>
<segment id ="2" name="Dendrite2">
<parent segment="1"/>
<distal x="30" y="0" z="0" diameter="1"/>
</segment>
<segment id ="3" name="Spine1">
<parent segment="2" fractionAlong="0.5"/>
<proximal x="25" y="0" z="0" diameter="0.1"/>
<distal x="25" y="0.2" z="0" diameter="0.1"/>
</segment>
<!-- segmentGroups follow -->
<segmentGroup id="soma_group" neuroLexId="sao1044911821"> <!-- Points to category "Neuronal Cell Body" in NeuroLex -->
<member segment="0"/>
</segmentGroup>
<segmentGroup id="dendrite_group" neuroLexId="sao1211023249"> <!-- Points to category "Dendrite" in NeuroLex -->
<member segment="1"/>
<member segment="2"/>
<member segment="3"/>
</segmentGroup>
<segmentGroup id="spines" neuroLexId="sao1145756102"> <!-- Points to category "Spine" in NeuroLex -->
<member segment="3"/>
</segmentGroup>
</morphology>
<biophysicalProperties id="bio_cell">
<membraneProperties>
<channelPopulation id="naChansDend" ionChannel="NaConductance" segment="2" number="120000" erev="50mV" ion="na"/> <!-- Use population instead of density -->
<channelDensity id="pasChans" ionChannel="pas" condDensity="3.0 S_per_m2" erev="-70mV" ion="non_specific"/> <!-- no segmentGroup => all segments! -->
<channelDensity id="naChansSoma" ionChannel="NaConductance" segmentGroup="soma_group" condDensity="120.0 mS_per_cm2" erev="50mV" ion="na"/>
<specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>
<specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>
</membraneProperties>
<intracellularProperties>
<resistivity value="0.1 kohm_cm"/> <!-- Used for specific axial resistance -->
</intracellularProperties>
</biophysicalProperties>
</cell>
</neuroml>