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;
//	PARAMETER FILE FOR NEURON 'block' : mitral cell model under
//		conditions of TEA and TTX block
//	Author : Upi Bhalla 
//	Mar 29 1991
//	Highly detailed model of mit cell with experimental averages for
//		cell geometry.


//	Format of file :
// x,y,z,dia are in microns, all other units are SI (Meter Kilogram Second Amp)
// In polar mode 'r' is in microns, theta and phi in degrees 
// Control line options start with a '*'
// The format for each compartment parameter line is :
//name	parent	r	theta	phi	d	ch	dens ...
//in polar mode, and in cartesian mode :
//name	parent	x	y	z	d	ch	dens ...

//		Coordinate mode
*cartesian
*relative

//		Specifying constants
*set_global	EREST_ACT	-0.065

///// Aditya translated Davison's Bhalla and Bower adapted 7 compartment model from Neuron into Genesis.
///// Davison's model has pseudo compartments interleaved within proper compartments soma, prim, glom and dend.
///// pseudo compartments have only Ra and negligible Cm and Rm.
//        #print self.Rs2d # 5154639 Ohms
//        #print self.Rs2p # 18281535.6 Ohms
//        #print self.Rp2g # 17064846 Ohms
// Ra = RA l / (pi r^2) = RA / (pi r^2), Rm = RM / (2 pi r l), Cm = CM * (2 pi r l) 
///// proper compartments have only Rm and Cm, negligible Ra.
///// But cannot set Ra, Rm, Cm values to less than 1e-15, hence CM = 1e-3. However, 1e-15 leads to numerical error accumulation so set reasonable values
///// This is done to ensure no difference between symmetric and asymmetric compartments.

*set_global	RA	1e-4
*set_global	CM	0.01
*set_global	RM	10
//soma	none	100	0	0	16	LCa3_mit_usb	40	K_mit_usb	28	KA_bsg_yka	58.7	Ca_mit_conc	5.2e-6	Kca_mit_usb	142	Na_mit_usb	1532	K2_mit_usb	1956
//LCa3_mit_usb causes a 15ms current transient with voltage clamp in mitral cell (Ca ionic channels might cause part of observed 'IPSC'.) - fig 2A left of Isaacson & Westbrook 1998.
//To remove double spikes, the fast first one of which does not propagate into the soma, can increase KA to 587 or LCa3 to 400.
soma	none	100	0	0	16	LCa3_mit_usb	40	K_mit_usb	28	KA_bsg_yka	58.7	Ca_mit_conc	5.2e-6	Kca_mit_usb	142	Na_mit_usb	1532	K2_mit_usb	1956

*set_global	RM	1e5
*set_global CM  1e-3
// set such that Rs2p # 18281535.6 Ohms
*set_global RA  57.433089
s2p	    soma	1	0	0	2

*set_global	RA	1e-4
*set_global	CM	0.01
*set_global	RM	10
//prim    s2p 	100	0	0	104	LCa3_mit_usb	22	K_mit_usb	17.4	K2_mit_usb	12.3	Na_mit_usb	13.4
// fast and full propagation along primary dendrite:
prim    s2p 	100	0	0	104	LCa3_mit_usb	10	K_mit_usb	17.4	K2_mit_usb	123	    Na_mit_usb	134

*set_global	RM	1e5
*set_global CM  1e-3
// set such that Rs2p # 17064846 Ohms
*set_global RA  53.6107495
p2g     prim    1   0   0   2

*set_global	RA	1e-4
*set_global	CM	0.01
*set_global	RM	10
// original bhalla and bower model had K_mit_usb as 28, but Davison used 200 as he says glom is too excitable. I also use 200.
//glom	p2g 	100	0	0	26.7	LCa3_mit_usb	95	K_mit_usb	28
glom	p2g 	100	0	0	26.7	LCa3_mit_usb	95	K_mit_usb	200
// I put below values to make mitral fire more and so that glom is less excitable - however it makes mitral double spike methinks.
//glom	p2g 	100	0	0	26.7	LCa3_mit_usb	20	K2_mit_usb	123 Na_mit_usb	134

*set_global	RM	1e5
*set_global CM  1e-3
// set such that Rs2p # 5154639 Ohms - use this Ra and the dia and len of dend below to get RA. Don't use this pseudo segment's dia and len
//*set_global RA  16.193762
// RA was too large, the lateral dendrite was not responding fast enough - too long time constant. See Margie et al 2000.
// Break lateral dendrite into two compartments
*set_global RA  16
s2d     soma    1   0   0   2

// after splitting into two, the electrotonic lengths have changed now.

*set_global	RA	1e-4
*set_global	CM	0.01
*set_global	RM	10
// Using Ra above and l and dia for dend below to get RA + using RM and dia of dend, lambda = 600microns. So electrotonic L of dend = 1/6.
// Compare with lambda of Upi's cell which is 1600 microns, and typical dendrite length is 850microns, hence L=0.5.
// Unlike BBmit1993, Davison doesn't have these LCa3_mit_usb and K_mit_usb in the dendrite!
//dend	s2d		100	0	0	170.9	LCa3_mit_usb	4	K_mit_usb	8.5	K2_mit_usb	226	Na_mit_usb	330
dend	s2d		100	0	0	170.9	LCa3_mit_usb	4	K_mit_usb	8.5	K2_mit_usb	226	Na_mit_usb	330

*set_global	RM	1e5
*set_global CM  1e-3
// set such that Rs2p # 5154639 Ohms - use this Ra and the dia and len of dend below to get RA. Don't use this pseudo segment's dia and len
//*set_global RA  16.193762
// RA was too large, the lateral dendrite was not responding fast enough - too long time constant. See Margie et al 2000.
// Break lateral dendrite into two compartments
*set_global RA  8
//s2d2     dend    1   0   0   2

*set_global	RA	1e-4
*set_global	CM	0.01
*set_global	RM	10
// Unlike BBmit1993, Davison doesn't have these LCa3_mit_usb and K_mit_usb in the dendrite!
//dend2	s2d2	50	0	0	170.9	LCa3_mit_usb	4	K_mit_usb	8.5	K2_mit_usb	226	Na_mit_usb	330

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