<?xml version="1.0" encoding="UTF-8"?>
<neuroml xmlns="http://morphml.org/neuroml/schema"
xmlns:mml="http://morphml.org/morphml/schema"
xmlns:nml="http://morphml.org/networkml/schema"
xmlns:meta="http://morphml.org/metadata/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/v1.8.0/Level3/NeuroML_Level3_v1.8.0.xsd"
name = "NeuroML Level 1, 2 and 3 PG cell model"
lengthUnits="micron">
<meta:notes>author: Aditya Gilra morphology adapted from Cleland and Sethupathy 2006,
channels set to get LTS behaviour as observed in McQuiston and Katz, 2001.</meta:notes>
<cells>
<cell name="PG">
<meta:notes>Cell: periglomerular morphml written by hand by Aditya Gilra, NCBS, Bangalore, India.</meta:notes>
<segments xmlns="http://morphml.org/morphml/schema"> <!-- Changing the namespace from neuroml to morphml-->
<!-- Section: soma -->
<segment id="0" name = "soma" cable = "0">
<proximal x="0" y="0" z="0" diameter="8"/>
<distal x="8" y="0" z="0" diameter="8"/>
</segment>
<!-- Section: dendrites -->
<segment id="1" name = "dend0" parent="0" cable = "1"> <!-- Connected at 1 on parent section: soma -->
<proximal x="8" y="0" z="0" diameter="1"/>
<distal x="28" y="0" z="0" diameter="1"/>
</segment>
<segment id="2" name = "dend1" parent="0" cable = "2"> <!-- Connected at 1 on parent section: soma -->
<proximal x="8" y="0" z="0" diameter="1"/>
<distal x="8" y="20" z="0" diameter="1"/>
</segment>
<!-- I don't really need the spines: just ensure that the soma EPSP is the same as with spines -->
<!--<segment id="3" name = "spineneck0" parent="1" cable = "3">
<proximal x="28" y="0" z="0" diameter="0.1"/>
<distal x="28.5" y="0" z="0" diameter="0.1"/>
</segment>
<segment id="4" name = "spinehead0" parent="3" cable = "4">
<proximal x="28.5" y="0" z="0" diameter="1"/>
<distal x="29" y="0" z="0" diameter="1"/>
</segment>
<segment id="5" name = "spineneck1" parent="2" cable = "5">
<proximal x="8" y="20" z="0" diameter="0.1"/>
<distal x="8" y="20.5" z="0" diameter="0.1"/>
</segment>
<segment id="6" name = "spinehead1" parent="5" cable = "6">
<proximal x="8" y="20.5" z="0" diameter="1"/>
<distal x="8" y="21" z="0" diameter="1"/>
</segment>-->
</segments>
<cables xmlns="http://morphml.org/morphml/schema"> <!-- Changing namespace from neuroml to morphml-->
<!--
<cable id="0" name="soma">
<meta:group>all</meta:group>
<meta:group>somagroup</meta:group>
</cable>
<cable id="1" name="dend0">
<meta:group>all</meta:group>
<meta:group>periphery</meta:group>
<meta:group>dendrites</meta:group>
</cable>
<cable id="2" name="dend1">
<meta:group>all</meta:group>
<meta:group>periphery</meta:group>
<meta:group>dendrites</meta:group>
</cable>
<cable id="3" name="spineneck0">
<meta:group>all</meta:group>
<meta:group>periphery</meta:group>
</cable>
<cable id="4" name="spinehead0">
<meta:group>all</meta:group>
<meta:group>periphery</meta:group>
<meta:group>spineheads</meta:group>
</cable>
<cable id="5" name="spineneck1">
<meta:group>all</meta:group>
<meta:group>periphery</meta:group>
</cable>
<cable id="6" name="spinehead1">
<meta:group>all</meta:group>
<meta:group>periphery</meta:group>
<meta:group>spineheads</meta:group>
</cable>
-->
<cable id="0" name="soma"/>
<cable id="1" name="dend0"/>
<cable id="2" name="dend1"/>
<!--<cable id="3" name="spineneck0"/>
<cable id="4" name="spinehead0"/>
<cable id="5" name="spineneck1"/>
<cable id="6" name="spinehead1"/>-->
<cablegroup name="all">
<cable id = "0"/>
<cable id = "1"/>
<cable id = "2"/>
<!--<cable id = "3"/>
<cable id = "4"/>
<cable id = "5"/>
<cable id = "6"/>-->
</cablegroup>
<cablegroup name="somagroup">
<cable id = "0"/>
</cablegroup>
<cablegroup name="dendrites">
<cable id = "1"/>
<cable id = "2"/>
</cablegroup>
<cablegroup name="ORNdendrite">
<cable id = "1"/>
</cablegroup>
<cablegroup name="periphery">
<cable id = "1"/>
<cable id = "2"/>
<!--<cable id = "3"/>
<cable id = "4"/>
<cable id = "5"/>
<cable id = "6"/>-->
</cablegroup>
<!--<cablegroup name="spineheads">
<cable id = "4"/>
<cable id = "6"/>
</cablegroup>-->
</cables>
<biophysics units='Physiological Units'>
<!-- Note: values of cond dens are different in NEURON and phy units-->
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' passive_conductance='true' type='Channel Mechanism' name='pas'>
<bio:parameter name='gmax' value='0.5'> <!-- 3 ms time constant with CM=1microF/cm^2 --><!-- 1GigaOhm for 8micron dia soma gives 0.5 mS/cm^2-->
<bio:group>all</bio:group>
</bio:parameter>
<bio:parameter name='e' value='-67'> <!-- -67mV sets RMP to -65.5 mV -->
<bio:group>all</bio:group>
</bio:parameter>
</bio:mechanism>
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='Na_rat_ms'>
<bio:parameter name='gmax' value='50'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='0'>
<bio:group>periphery</bio:group>
</bio:parameter>
</bio:mechanism>
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='K2_mit_usb'>
<bio:parameter name='gmax' value='50'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='0'>
<bio:group>periphery</bio:group>
</bio:parameter>
<bio:parameter name='e' value='-80'>
<bio:group>all</bio:group>
</bio:parameter>
</bio:mechanism>
<!--<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='K_mit_usb'>
<bio:parameter name='gmax' value='0.0'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='0.0'>
<bio:group>periphery</bio:group>
</bio:parameter>
</bio:mechanism>-->
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='Ih_cb'>
<bio:parameter name='gmax' value='6.0'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='0'>
<bio:group>periphery</bio:group>
</bio:parameter>
</bio:mechanism>
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='TCa_d'>
<bio:parameter name='gmax' value='60.0'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='0'>
<bio:group>periphery</bio:group>
</bio:parameter>
</bio:mechanism>
<!--<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='KA_bsg_yka'>
<bio:parameter name='gmax' value='0.0'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='0.0'>
<bio:group>periphery</bio:group>
</bio:parameter>
<bio:parameter name='e' value='-80'>
<bio:group>all</bio:group>
</bio:parameter>
</bio:mechanism>-->
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Ion Concentration' name='Ca_mit_conc'>
<!-- Book of Genesis Chapter 12 mentions that B must often be reduced by a factor > 100
to take buffering into account. Here that factor 100 is just clubbed into the depth.
Each values of depth is actually 0.1 micron * 100 for buffering.
This is a hack. Ideally there should be a buffering factor tag. -->
<bio:parameter name='depth' value='10'>
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name='depth' value='10'>
<bio:group>dendrites</bio:group>
</bio:parameter>
<!--<bio:parameter name='depth' value='20'>
<bio:group>spineheads</bio:group>
</bio:parameter>-->
</bio:mechanism>
<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type="Channel Mechanism" name="Kca_mit_usb_pg">
<bio:parameter name="gmax" value="6.0">
<bio:group>somagroup</bio:group>
</bio:parameter>
<bio:parameter name="gmax" value="0.0">
<bio:group>periphery</bio:group>
</bio:parameter>
</bio:mechanism>
<!-- capacitance and axial resistance and init_memb_potential must be at the very end! Order is important! -->
<bio:spec_capacitance xmlns:bio='http://morphml.org/biophysics/schema'>
<bio:parameter value='1.0'>
<bio:group>all</bio:group>
</bio:parameter>
</bio:spec_capacitance>
<bio:spec_axial_resistance xmlns:bio='http://morphml.org/biophysics/schema'>
<bio:parameter value='0.2'>
<bio:group>all</bio:group>
</bio:parameter>
</bio:spec_axial_resistance>
<bio:init_memb_potential>
<bio:parameter value="-65">
<bio:group>all</bio:group>
</bio:parameter>
</bio:init_memb_potential>
</biophysics>
<connectivity>
<nml:potential_syn_loc xmlns="http://networkml.org/ml/schema" synapse_type="ORN_PG" synapse_direction="post">
<!--<nml:group>spineheads</nml:group>-->
<nml:group>dendrites</nml:group>
<!--<nml:group>ORNdendrite</nml:group>-->
</nml:potential_syn_loc>
<nml:potential_syn_loc xmlns="http://networkml.org/ml/schema" synapse_type="mitral_PG" synapse_direction="post">
<!--<nml:group>spineheads</nml:group>-->
<nml:group>dendrites</nml:group>
</nml:potential_syn_loc>
<nml:potential_syn_loc xmlns="http://networkml.org/ml/schema" synapse_type="PG_mitral" synapse_direction="pre">
<!--<nml:group>somagroup</nml:group>-->
<nml:group>dendrites</nml:group>
</nml:potential_syn_loc>
<nml:potential_syn_loc xmlns="http://networkml.org/ml/schema" synapse_type="SA_PG" synapse_direction="post">
<nml:group>dendrites</nml:group>
</nml:potential_syn_loc>
</connectivity>
</cell>
</cells>
</neuroml>
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