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]
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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
cells
PG_nrn
readme.txt *
hpg.mod *
kamt.mod *
kdrmt.mod *
naxn.mod *
nmdanetOB.mod *
TCa_d.mod *
coeff-table.txt *
forfig3.hoc *
gc.hoc *
Level2.xml
mitral.hoc *
mitral_davison2007_neurml_L1.xml
mod_func.c
mosinit.hoc *
nrnmech.dll
PGsimple_aditya2010_neuroML_L1_L2.xml
PGTest_nrn.py
                            
TITLE Low threshold calcium current
:
:   Ca++ current responsible for low threshold spikes (LTS)
:   RETICULAR THALAMUS
:   Differential equations
:
:   Model of Huguenard & McCormick, J Neurophysiol 68: 1373-1383, 1992.
:   The kinetics is described by standard equations (NOT GHK)
:   using a m2h format, according to the voltage-clamp data
:   (whole cell patch clamp) of Huguenard & Prince, J Neurosci.
:   12: 3804-3817, 1992.
:   See also: http://www.cnl.salk.edu/~alain ,  http://cns.fmed.ulaval.ca
:
:    - Kinetics adapted to fit the T-channel of reticular neuron
:    - Q10 changed to 5 and 3
:    - Time constant htau fitted from experimental data
:    - shift parameter for screening charge
:
:   ACTIVATION FUNCTIONS FROM EXPERIMENTS (NO CORRECTION)
:
:   Reversal potential taken from Nernst Equation
:
:   Written by Alain Destexhe, Salk Institute, Sept 18, 1992
:

INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}

NEURON {
	SUFFIX TCa_d
	USEION ca READ cai, cao WRITE ica
	RANGE gmax, shift : aditya changed gcabar to gmax
	GLOBAL minf, mtau, hinf, htau : aditya shifted these from RANGE to GLOBAL for ease in plotting them
}

UNITS {
	(molar) = (1/liter)
	(mV) =	(millivolt)
	(mA) =	(milliamp)
	(mM) =	(millimolar)

	FARADAY = (faraday) (coulomb)
	R = (k-mole) (joule/degC)
}

PARAMETER {
	v		(mV)
	celsius	= 36	(degC) : aditya - this will be overridden by external global celsius anyway
:	eca	= 120	(mV)
	gmax	= .0008	(mho/cm2)
	shift	= 0 	(mV)
	cai	: aditya put the default values in INITIAL block
	cao	: aditya put the default values in INITIAL block
}

STATE {
	m h
}

ASSIGNED {
	ica	(mA/cm2)
	carev	(mV)
	minf
	mtau	(ms)
	hinf
	htau	(ms)
	phi_m
	phi_h
}

BREAKPOINT {
	SOLVE castate METHOD euler
	carev = (1e3) * (R*(celsius+273.15))/(2*FARADAY) * log (cao/cai)
	ica = gmax * m*m*h * (v-carev)
}

DERIVATIVE castate {
	evaluate_fct(v)

	m' = (minf - m) / mtau
	h' = (hinf - h) / htau
}

UNITSOFF
INITIAL {
:
:   Activation functions and kinetics were obtained from
:   Huguenard & Prince, and were at 23-25 deg.
:   Transformation to 36 deg assuming Q10 of 5 and 3 for m and h
:   (as in Coulter et al., J Physiol 414: 587, 1989)
:
	cai	= 2.4e-4 (mM)		: adjusted for eca=120 mV : aditya put them in INITIAL block so that they don't need to be supplied externally
	cao	= 2	(mM)    : aditya put them in INITIAL block so that they don't need to be supplied externally

	phi_m = 5.0 ^ ((celsius-24)/10)
	phi_h = 3.0 ^ ((celsius-24)/10)

	evaluate_fct(v)

	m = minf
	h = hinf
}

PROCEDURE evaluate_fct(v(mV)) { 
:
:   Time constants were obtained from J. Huguenard
:

	minf = 1.0 / ( 1 + exp(-(v+shift+50)/7.4) )
	hinf = 1.0 / ( 1 + exp((v+shift+78)/5.0) )

	mtau = ( 3 + 1.0 / ( exp((v+shift+25)/10) + exp(-(v+shift+100)/15) ) ) / phi_m
	htau = ( 85 + 1.0 / ( exp((v+shift+46)/4) + exp(-(v+shift+405)/50) ) ) / phi_h
}
UNITSON