root/NeuroML2/examples/NML2_FullCell.nml

<?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_v2alpha.xsd"
    id="NML2_FullCell">
        

<!-- Example of a multicompartmental cell with biophysics in NeuroML 2 -->

<!-- This is a "pure" NeuroML 2 file. It cannot yet be used a simulation by the LEMS 
     Interpreter as this does not yet support multicompartment cells -->   


    <include href="SimpleIonChannel.xml"/> <!-- Contains ionChannel NaConductance -->

    <!-- 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:isVersionOf>
                  <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:isVersionOf>
              </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"/>   <!-- Use population instead of density -->

                <channelDensity id="pasChans" ionChannel="pas" condDensity="3.0 S_per_m2"/> <!-- no segmentGroup => all segments! -->

                <channelDensity id="naChansSoma" ionChannel="NaConductance" segmentGroup="soma_group" condDensity="120.0 mS_per_cm2"/>

                <specificCapacitance segmentGroup="soma_group" value="1.0 uF_per_cm2"/>

                <specificCapacitance segmentGroup="dendrite_group" value="2.0 uF_per_cm2"/>

                <reversalPotential species="na" value="55mV"/>

            </membraneProperties>

            <intracellularProperties>

                <!-- Ions present inside the cell. -->
                <species id="ca">
                    <fixedConcentration  concentration="1e-5 mM"/>
                </species>

                <resistivity value="0.1 kohm_cm"/>  <!-- Used for specific axial resistance -->

            </intracellularProperties>

        </biophysicalProperties>


    </cell>

</neuroml>