Olfactory bulb microcircuits model with dual-layer inhibition (Gilra & Bhalla 2015)

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Accession:153574
A detailed network model of the dual-layer dendro-dendritic inhibitory microcircuits in the rat olfactory bulb comprising compartmental mitral, granule and PG cells developed by Aditya Gilra, Upinder S. Bhalla (2015). All cell morphologies and network connections are in NeuroML v1.8.0. PG and granule cell channels and synapses are also in NeuroML v1.8.0. Mitral cell channels and synapses are in native python.
Reference:
1 . Gilra A, Bhalla US (2015) Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. PLoS One 10:e0098045 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell;
Channel(s): I A; I h; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s): AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: Python; MOOSE/PyMOOSE;
Model Concept(s): Sensory processing; Sensory coding; Markov-type model; Olfaction;
Implementer(s): Bhalla, Upinder S [bhalla at ncbs.res.in]; Gilra, Aditya [aditya_gilra -at- yahoo -period- com];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron periglomerular GABA cell; Olfactory bulb main interneuron granule MC GABA cell; AMPA; NMDA; Gaba; I A; I h; I K,Ca; I Sodium; I Calcium; I Potassium; Gaba; Glutamate;
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    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 adapted from Cleland and Sethupathy 2006.</meta:notes>

<cells>
  <cell name="PG_LTS">
    <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">
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      <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>
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      <cable id="2" name="dend1">
        <meta:group>all</meta:group>
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      <cable id="3" name="spineneck0">
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      <cable id="4" name="spinehead0">
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      <cable id="5" name="spineneck1">
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      <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 mV -->
            <bio:group>all</bio:group>
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        </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>
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          <bio:parameter name='gmax' value='0'>
            <bio:group>periphery</bio:group>
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        <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>
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          <bio:parameter name='gmax' value='0'>
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          <bio:parameter name='e' value='-80'>
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        <!--<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>
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          <bio:parameter name='gmax' value='0.0'>
            <bio:group>periphery</bio:group>
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        <!--<bio:mechanism xmlns:bio='http://morphml.org/biophysics/schema' type='Channel Mechanism' name='KA_bsg_yka'>
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          <bio:parameter name='gmax' value='0.0'>
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          <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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