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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olfactory-bulb-gilra-bhalla
channels
neuron_channels
CaHVA_Chan.xml
CaL_Chan.xml
CaLChannel.py
CaPool.py
CaTChannel.py
channelConstants.py
granuleDefaults.py
Ih_cb.xml
KAChannel.py
KAChannelMS.py
KCaA.dat
KCaA_PG.dat
KCaB.dat
KCaB_PG.dat
KCaChannel.py
KCaChannel_PG.py
KCaMPIChannel.py
KCaMPIChannel_PG.py
KDRChannelMS.py
kfast_k.inf *
kfast_k.tau *
kfast_n.inf *
kfast_n.tau *
KFastChannel.py
KMChannel.py
kslow_k.inf *
kslow_k.tau *
kslow_n.inf *
kslow_n.tau *
KSlowChannel.py
load_channels.py
MOOSEChannelTest.py
NaChannel.py
NaGranChannel.py
NaMitChannelMS.py
tabchannels.dat *
TCa_d.xml
                            
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import math

# The PYTHONPATH should contain the location of moose.py and _moose.so
# files.  Putting ".." with the assumption that moose.py and _moose.so
# has been generated in ${MOOSE_SOURCE_DIRECTORY}/pymoose/ (as default
# pymoose build does) and this file is located in
# ${MOOSE_SOURCE_DIRECTORY}/pymoose/examples
# sys.path.append('..\..')
try:
    import moose
except ImportError:
    print "ERROR: Could not import moose. Please add the directory containing moose.py in your PYTHONPATH"
    import sys
    sys.exit(1)

from channelConstants import *

VKCa = -80.0e-3 # Volts # kca3.mod has a vshift=-10mV in addition to ek=-70mV

GKCa = 142.0*sarea # Siemens, from mit4.hoc

def calc_KCa_PG_alpha_y(v,Ca):
    #return math.exp((v-65e-3)/27e-3) * 500.0e3*(0.015-Ca)/(math.exp((0.015-Ca)/0.0013)-1) # This is from Bhalla and Bower's 1993 paper: perhaps the v-65e-3 is a typo. It should be as below.
    #return math.exp((v+70e-3)/27e-3)*1e3 * 500.0*(0.015-Ca)/(math.exp((0.015-Ca)/0.0013)-1) # This is from kca3.mod: different from Bhalla and Bower 1993 paper. see above
    ## Changed the Ca half point for the PG cell as I reduced B by 100 to get intracellular Ca conc to reasonable levels.
    return math.exp((v+70e-3)/27e-3)*1e3 * 500.0*(0.0055-Ca)/(math.exp((0.0055-Ca)/0.0013)-1)

def calc_KCa_PG_beta_y(v,Ca):
    return 0.05e3

CaMIN = 0.0
CaMAX = 1.0e-2 # mol/m^2 same as millimol/litre
CaNDIVS = 100

class KCaChannel_PG(moose.HHChannel2D):
    """KCa_PG channel inherits from HHChannel2D."""
    def __init__(self, *args):
        """Setup the KCa channel with defaults"""
        moose.HHChannel2D.__init__(self,*args)
        ### Since this channel is table based and this script is for creation of KCaA_PG.dat and KCaB_PG.dat,
        ### while KCaMPIChannel_PG.py is for reading in these tables,
        ### we hard code the VMIN, VMAX and NDIVS so that those in globalConstants.py
        ### do not spoil the reading in of already created tables.
        VMIN = -0.1 # V
        VMAX = 0.05 # V
        NDIVS = 150
        dv = (VMAX-VMIN)/NDIVS
        ## For HHChannel2D Ek, Gbar, etc don't get set via python assignments!!!
        ## Have to use moose shell commands.
        #self.Ek = VKCa
        self.getContext().runG('setfield '+self.path+' Ek '+str(VKCa))
        #self.Gbar = GKCa
        self.getContext().runG('setfield '+self.path+' Gbar '+str(GKCa))
        self.addField('ion')
        self.setField('ion','K')
        self.addField('ionDependency')
        self.setField('ionDependency','Ca')
        ## This will create HHGate2D instance xGate inside the KCa channel.
        ## (2D since it is within HHChannel2D)
        self.Xpower = 1
        ## VOLT_C1_INDEX: VOLTAGE message specifies x variable
        ## and CONCEN1 variable specifies y variable of X_A and X_B tables;
        ## pg 323, sec 19.4.6 of Book of Genesis
        self.Xindex = "VOLT_C1_INDEX"
        ## xGate was already created and wrapped when Xpower was set non-zero
        #self.xGate = moose.HHGate2D(self.path + "/xGate")
        #self.getContext().runG("showfield "+self.path +"/xGate/A -all")
        self.xGate.A.xmin = VMIN
        self.xGate.A.xmax = VMAX
        #self.xGate.A.xdivs = NDIVS # these get overridden by the number of values in the table
        self.xGate.B.xmin = VMIN
        self.xGate.B.xmax = VMAX
        #self.xGate.B.xdivs = NDIVS # these get overridden by the number of values in the table

        ### HHGate2D is not wrapped properly in pyMOOSE.
        ### ymin, ymax and ydivs are not exposed.
        ### Setting them creates new and useless attributes within HHGate2D without warning!
        ### Hence use runG to set these via Genesis command
        self.getContext().runG("setfield "+self.path+"/xGate/A"+\
            #" ydivs "+str(CaNDIVS)+\ # these get overridden by the number of values in the table
            " ymin "+str(CaMIN)+\
            " ymax "+str(CaMAX))
        self.getContext().runG("setfield "+self.path+"/xGate/B"+\
            #" ydivs "+str(CaNDIVS)+\ # these get overridden by the number of values in the table
            " ymin "+str(CaMIN)+\
            " ymax "+str(CaMAX))

        selfdir = os.path.dirname(__file__)
        if selfdir != '': selfdir += os.sep
        ftableA = open(selfdir+"KCaA_PG.dat","w")
        ftableB = open(selfdir+"KCaB_PG.dat","w")
        v = VMIN
        dCa = (CaMAX-CaMIN)/CaNDIVS
        for i in range(NDIVS+1):
            Ca = CaMIN
            for j in range(CaNDIVS+1):
                alpha = calc_KCa_PG_alpha_y(v,Ca)
                ftableA.write(str(alpha)+" ")
                ftableB.write(str(alpha+calc_KCa_PG_beta_y(v,Ca))+" ")
                Ca += dCa
            ftableA.write("\n")
            ftableB.write("\n")
            v += dv
        ftableA.close()
        ftableB.close()

        ### PRESENTLY, Interpol2D.cpp in MOOSE only allows loading via a data file,
        ### one cannot set individual entries A[0][0] etc.
        ### Thus pyMOOSE also has not wrapped Interpol2D
        self.getContext().runG("call "+self.path+"/xGate/A load "+selfdir+"KCaA_PG.dat 0")
        self.getContext().runG("call "+self.path+"/xGate/B load "+selfdir+"KCaB_PG.dat 0")
        
        # Test print of table
        #self.getContext().runG("call "+self.path+"/xGate/A print "+selfdir+"KCaA_out.dat")
        #self.getContext().runG("call "+self.path+"/xGate/B print "+selfdir+"KCaB_out.dat")

        # calc_mode is LIN_INTERP i.e. 1 by default, so no need to set it as below.
        #self.getContext().runG("setfield "+self.path+" X_A->calc_mode 1")
        #self.getContext().runG("setfield "+self.path+" X_B->calc_mode 1")


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