<?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 Cell Level 1, 2, 3 file written by Aditya Gilra"
lengthUnits="micron">
<meta:notes>author: Aditya Gilra adapted from Migliore and Shepherd 2008.</meta:notes>
<cells>
<cell name="granule">
<meta:notes>Cell: granule morphml written by hand by Aditya.</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"> <!-- soma is somagc of gc.hoc of Migliore and Shepherd 2008. -->
<proximal x="0" y="0" z="0" diameter="8"/>
<distal x="0" y="0" z="8" diameter="8"/>
</segment>
<!-- Section: periphery -->
<segment id="1" name = "periphery" parent="0" cable = "1"> <!-- periphery is priden of gc.hoc of Migliore and Shepherd 2008. -->
<proximal x="0" y="0" z="8" diameter="0.5"/>
<distal x="0" y="0" z="258" diameter="0.5"/>
</segment>
<!-- I have left out all the other dendrites priden2[] of 100 micron length in Migliore and Shepherd.
So, I increased the priden i.e. periphery length to 250 microns instead of 150microns. -->
<!-- Sub-linear summation perhaps because of same dendrite -->
</segments>
<cables xmlns="http://morphml.org/morphml/schema"> <!-- Changing namespace from neuroml to morphml-->
<cable id = "0" name = "soma" fract_along_parent = "0"/>
<cable id = "1" name = "periphery" fract_along_parent = "1"/>
<cablegroup name="all">
<cable id = "0"/>
<cable id = "1"/>
</cablegroup>
<cablegroup name="soma">
<cable id = "0"/>
</cablegroup>
<cablegroup name="periphery">
<cable id = "1"/>
</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'>
<!-- Both Migliore and Shepherd 2008 and Egger et al 2003 say taum = 30ms, Rin=1GOhm. So set RM and CM for it.
See however, Carleton et al 2003 who have taum=14ms in mice,
and Cang&Isaacson2003 have much sharper mit->gran EPSPs than obtained by taum=30ms. -->
<bio:parameter name='gmax' value='0.13333'> <!-- RM = 30e-3/CM = 0.75 Ohm-m^2. Thus GM = 1/0.75 = 1.3333 S/m^2 = 0.13333 mS/cm^2 -->
<bio:group>all</bio:group>
</bio:parameter>
<bio:parameter name='e' value='-65'>
<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='25'> <!-- 400 S/m^2 = 40 mS/cm^2-->
<bio:group>soma</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='10'> <!-- 200 S/m^2 = 20 mS/cm^2-->
<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='10'>
<bio:group>soma</bio:group>
</bio:parameter>
<bio:parameter name='gmax' value='5'>
<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='KA_ms'>
<bio:parameter name='gmax' value='15'> <!-- 100 S/m^2 = 10 mS/cm^2-->
<bio:group>soma</bio:group>
</bio:parameter>
<!-- Following Migliore and Shepherd 2008, I have only KA and not KDR in dendrites!
This is supposed to cause spike latency. -->
<!-- Not too useful for me, since I club granules together,
but still good to have differential latency -->
<!-- Dunno if latency actually works with only one 'periphery' dendrite -->
<bio:parameter name='gmax' value='10.0'> <!-- 80 S/m^2 = 8 mS/cm^2-->
<bio:group>periphery</bio:group>
</bio:parameter>
<bio:parameter name='e' value='-80'>
<bio:group>all</bio:group>
</bio:parameter>
</bio:mechanism>
<bio:spec_capacitance xmlns:bio='http://morphml.org/biophysics/schema'>
<bio:parameter value='4'> <!-- CM = 0.04 F/m^2 = 4 microF/cm^2 : Seems too high compared to usual 0.01 F?m^2! -->
<bio:group>all</bio:group>
</bio:parameter>
</bio:spec_capacitance>
<bio:spec_axial_resistance xmlns:bio='http://morphml.org/biophysics/schema'>
<bio:parameter value='0.08'> <!-- 0.8 Ohm-m = 0.08 KOhm-cm -->
<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>
<!-- These synapse_types do not correspond to actual synapses in /library.
Rather, they must be used by network generators to map these synapse_types into say AMPA/NMDA etc.
In any case, these only represent potential locations and not actually realized ones. -->
<nml:potential_syn_loc synapse_type="mitral_granule" synapse_direction="post">
<nml:group>periphery</nml:group> <!-- periphery compartments -->
</nml:potential_syn_loc>
<nml:potential_syn_loc synapse_type="granule_mitral" synapse_direction="pre">
<nml:group>periphery</nml:group> <!-- periphery compartments -->
</nml:potential_syn_loc>
</connectivity>
</cell>
</cells>
</neuroml>
| 
