<?xml version="1.0" encoding="UTF-8"?>
<neuroml xmlns="http://morphml.org/neuroml/schema"
xmlns:nml="http://morphml.org/neuroml/schema"
xmlns:meta="http://morphml.org/metadata/schema"
xmlns:mml="http://morphml.org/morphml/schema"
xmlns:bio="http://morphml.org/biophysics/schema"
xmlns:cml="http://morphml.org/channelml/schema"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://morphml.org/neuroml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level2/NeuroML_Level2_v1.8.1.xsd"
length_units="micrometer">
<cells>
<cell name="InhomogenousBiophys">
<meta:notes>A cell with some inhomogenous biophysical parameters. </meta:notes>
<segments xmlns="http://morphml.org/morphml/schema">
<segment id="0" name="Soma" cable="0">
<proximal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
<distal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
</segment>
<segment id= "1" name = "DendSeg1" parent = "0" cable = "1">
<proximal x="0" y="0" z="0" diameter="5"/>
<distal x="0" y="10" z="0" diameter="5"/>
</segment>
<segment id= "2" name = "DendSeg2" parent = "1" cable = "1">
<distal x="0" y="20" z="0" diameter="5"/>
</segment>
<segment id= "3" name = "DendSeg3" parent = "2" cable = "2">
<proximal x="0" y="20" z="0" diameter="5"/>
<distal x="0" y="100" z="0" diameter="5"/>
</segment>
<segment id= "4" name = "DendSeg4" parent = "3" cable = "2">
<distal x="0" y="200" z="0" diameter="5"/>
</segment>
</segments>
<cables xmlns="http://morphml.org/morphml/schema">
<cable id="0" name="Soma"/>
<cable id= "1" name = "DendSection1"/>
<cable id= "2" name = "DendSection2">
<meta:properties>
<meta:property>
<meta:tag>numberInternalDivisions</meta:tag>
<meta:value>4</meta:value>
</meta:property>
</meta:properties>
</cable>
<cablegroup name="all">
<cable id="0"/>
<cable id="1"/>
<cable id="2"/>
</cablegroup>
<cablegroup name="soma_group">
<cable id="0"/>
</cablegroup>
<cablegroup name="dendrite_group">
<cable id="1"/>
<cable id="2"/>
<!-- A parameter whose value varies from 0 at the start of the group closest to the soma
to 1 at the most distal point of the segments in the group.-->
<inhomogeneous_param name="dendrite_group_x1" variable="p">
<metric>Path Length from root</metric>
<proximal translationStart="0"/>
<distal normalizationEnd="1"/>
</inhomogeneous_param>
<!-- A parameter whose value varies from 0 at the start of the group closest to the soma (as its attached to the soma)
to 200 at the most distal point of the segments in the group.-->
<inhomogeneous_param name="dendrite_group_x2" variable="p">
<metric>Path Length from root</metric>
</inhomogeneous_param>
</cablegroup>
</cables>
<!--Adding the biophysical parameters. Note element biophysics is in nml namespace, but the elements inside
are in http://morphml.org/biophysics/schema namespace (in Biophysics_v*.*.xsd)-->
<nml:biophysics units="Physiological Units" xmlns="http://morphml.org/biophysics/schema">
<mechanism name="PassiveCond" type="Channel Mechanism">
<parameter name="gmax" value="0.03">
<group>soma_group</group>
</parameter>
<variable_parameter name="gmax">
<!-- Will result in a gmax of 0.2 at soma end, 0.1 at other end-->
<group>dendrite_group</group>
<inhomogeneous_value param_name="dendrite_group_x2" value="0.2 - 0.1(p/200)"/>
</variable_parameter>
</mechanism>
<mechanism name="NaConductance" type="Channel Mechanism">
<variable_parameter name = "gmax">
<group>dendrite_group</group>
<inhomogeneous_value param_name="dendrite_group_x1" value="50 * (1-(p/2))"/>
</variable_parameter>
</mechanism>
<spec_capacitance>
<parameter value="1">
<group>all</group>
</parameter>
</spec_capacitance>
<spec_axial_resistance>
<parameter value="0.11">
<group>all</group>
</parameter>
</spec_axial_resistance>
</nml:biophysics>
</cell>
</cells>
</neuroml>
|
