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;
from synapseConstantsMinimal import *

############# ORN to mitral!
############# Set these such that 100 ORNs at approx 50Hz make the mitral cell fire in the middle of its linear range.
#SYN_EXC_G = 1 * 8.6516e-9 # Siemens
#SYN_INH_G = 1 * 2.2126e-9 # Siemens

GRANULE_INH_GRADED = False#True

RECEPTOR_SATURATION = 1.0#0.5 # Needed for single synapse KinSynChan and also in the baseline SynChan to correct for usage of synaptic weights across synchan and kinsynchan.
#RECEPTOR_SATN_CORRECTN_NMDA = 0.8785 # above 6mV EPSP #0.22 #for CM=0.04 #0.25 #for CM=0.01 #0.275 # See my onenote notes dt03/07/2010 for derivation of this value.
#RECEPTOR_SATN_CORRECTN_AMPA = 1.0818 # above 6mV EPSP #0.35 #0.19 # See my onenote notes dt03/07/2010 for derivation of this value.
RECEPTOR_SATN_CORRECTN_NMDA = 0.892 #4mV EPSP #0.22 #for CM=0.04 #0.25 #for CM=0.01 #0.275 # See my onenote notes dt03/07/2010 for derivation of this value.
RECEPTOR_SATN_CORRECTN_AMPA = 1.069 #4mV EPSP #0.35 #0.19 # See my onenote notes dt03/07/2010 for derivation of this value.
#RECEPTOR_SATN_CORRECTN_NMDA = 0.9397 #7mV EPSP with CM=0.02 #0.22 #for CM=0.04 #0.25 #for CM=0.01 #0.275 # See my onenote notes dt03/07/2010 for derivation of this value.
#RECEPTOR_SATN_CORRECTN_AMPA = 1.0679 #7mV EPSP with CM=0.02 #0.35 #0.19 # See my onenote notes dt03/07/2010 for derivation of this value.

## Arevian et al's activity dep inhibition work is under physiological conditions 
## i.e. 1mM Mg. as also Urban's previous work.
MG_CONC = 1.0 #0.001 #1.3 #mM SI units mol/m^3 = mmol/liter = mMolar (mM) # value of 1.3 mM From Isaacson 2001 PNAS; [Mg++] should be non-zero, hence 0.001 for 0.0
## Giridhar et al use no Mg2+, hence this setting for testing asymmetrical lateral inhibition
#MG_CONC = 0.1 #0.001 #1.3 #mM SI units mol/m^3 = mmol/liter = mMolar (mM) # value of 1.3 mM From Isaacson 2001 PNAS; [Mg++] should be non-zero, hence 0.001 for 0.0

mitral_granule_AMPA_Ek = 0.0 # Volts
## below is imported from synapseConstantsMinimal.py
#mitral_granule_AMPA_Gbar = 0.35e-9#0.35e-9 # Siemens ## This has been set so as to get roughly 8mV near the 12mV EPSP of Trombley & Shepherd 1992 JNeurosci
mitral_granule_saturatingAMPA_Gbar = 0.35e-9/RECEPTOR_SATN_CORRECTN_AMPA# Siemens ## This has been set so as to get roughly 8mV near the 12mV EPSP of Trombley & Shepherd 1992 JNeurosci
# From Cang and Isaacson 2003, in-vivo whole cell sEPSP data: 1ms rise and 4ms decay.
mitral_granule_AMPA_tau1 = 1.0e-3#2.0e-3 # seconds # Davison etal 2003 assume instantaneous rise but write that 4 ms is experimental, but is this for AMPA or GABA!
mitral_granule_AMPA_tau2 = 4.0e-3#5.5e-3 # seconds # decay time - from Migliore and Shepherd 2008.
mitral_granule_saturatingAMPA_pulseWidth = mitral_granule_AMPA_tau1 # this is the time to peak for KinSynChan
mitral_granule_saturatingAMPA_tau1 = mitral_granule_AMPA_tau2 # saturating syn decay time - roughly from fig 1B of Migliore and Shepherd 2008.
mitral_granule_saturatingAMPA_rInf = RECEPTOR_SATURATION # make some receptors saturate - set it so that it is best for lateral inhibition.

mitral_granule_NMDA_Ek = 0.0 # Volts
mitral_granule_NMDA_Gbar = 0.26*mitral_granule_AMPA_Gbar #0.1e-9 # Siemens ## This has been set so as to get roughly 8mV near the 12mV EPSP of Trombley & Shepherd 1992 JNeurosci
mitral_granule_saturatingNMDA_Gbar = 0.26*mitral_granule_AMPA_Gbar/RECEPTOR_SATN_CORRECTN_NMDA # Siemens ## This has been set so as to get roughly 8mV near the 12mV EPSP of Trombley & Shepherd 1992 JNeurosci
##### For SynChan
mitral_granule_NMDA_tau1 = 25e-3#20e-3 # rise time
mitral_granule_NMDA_tau2 = 200e-3#50e-3 # decay time - roughly from Migliore and Shepherd 2008.
##### For KinSynChan - rinf - fraction open due to a transmitter release and tau1 - decay time
mitral_granule_saturatingNMDA_pulseWidth = mitral_granule_NMDA_tau1 # this is the time to peak for KinSynChan
mitral_granule_saturatingNMDA_tau1 = mitral_granule_NMDA_tau2 # decay time - roughly from Migliore and Shepherd 2008.
mitral_granule_saturatingNMDA_rInf = RECEPTOR_SATURATION # make some receptors saturate - first pass set it so that it is best for lateral inhibition.
mitral_granule_NMDA_KMg_A = 1.0/0.1 #1.0/0.33 # mM
mitral_granule_NMDA_KMg_B = 1.0/73.0 #1.0/60.0 # V
mitral_granule_NMDA_MgConc = MG_CONC

## Choose between using a short-term plastic synapse or a non-plastic synapse.
GABA_plastic = False
GABA_depression_factor = 0.8 # should be 0.5 from Murthy's 2005 paper but aggregated synapses (?)
GABA_recovery_time = 6.0 # seconds # From Venki Murthy's 2005 paper.

granule_mitral_GABA_Ek = -0.078 # Volts
#### averaged inhibitory synapse:
#granule_mitral_GABA_Gbar = 0.6e-9 # Siemens
#granule_mitral_GABA_tau1 = 50e-3 # averaged IPSP from Urban and Sakmann 2002 #1e-3 # seconds # Davison etal 2003 assume instantaneous rise but write that 4 ms is experimental, but is this for AMPA or GABA!
#granule_mitral_GABA_tau2 = 75e-3 # averaged IPSP from Urban and Saknann 2002 #10e-3 # seconds # roughly from fig 2A of Isaacson and Strowbridge 1998.
#### unitary inhibitory synapse:
## below are imported from synapseConstantsMinimal.py
#granule_mitral_GABA_Gbar = 10e-9#15e-9#2e-9 # Siemens
#self_mitral_GABA_Gbar = 50e-12 # Siemens
granule_mitral_GABA_tau1 = 1e-3#3e-3 # roughly from fig 1C of Schoppa et al 1998
granule_mitral_GABA_tau2 = 20e-3#1e-3#20e-3 # from text and fig 1C of Schoppa et al 1998