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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<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>

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