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;
# -*- coding: utf-8 -*-
# ALL SI UNITS
# milliMolar is same as mol/m^3

## These are the simulation parameters for testing activity dependent inhibition between two mitrals via granules
## Only 2 gloms, 2 mitral sisters per glom.

from pylab import *
rc('path',simplify= False) # To ensure matplotlib connects points at expense of speed.

## assuming sys.path already has '../networks'
from networkConstants import * # has SETTLETIME, PULSE_RUNTIME, pulsebins
## below file is programmatically generated for repeats with different params.
from simset_activinhibition_minimal import *

SIMDT = 5e-5 # seconds
## Correction factor for event-based vs graded synchans
## In event-based case, activation = weight/simdt while in graded case activation is used directly.
## Further, due to every sim point in graded case acting like an event,
## moose gives a convolved Gk which is much larger (say 1000 times) than the event based one.
## So I should correct for simdt and the activation weighted multiple events at every simdt.
#synchan_activation_correction = 1/SIMDT / 1000 # for SIMDT=1e-5
synchan_activation_correction = 1/SIMDT / 250 # for SIMDT=5e-5

PLOTDT = 5e-5 # seconds
## add SETTLETIME from stimuliConstants.py to the REALRUNTIME to get the simulation RUNTIME
## very important to use 400ms stimulus (a la Arevian),
## as the granule starts firing after 400ms for ~100Hz
REALRUNTIME = 0.4 # seconds - for active inhibition - stimulus only for 400ms

VOLTAGE_CLAMP = False

NUMBINS = 10
###### Somehow mpiexec doesn't like number of processes > 1000 and
###### gives errors somewhere in the middle of the run
###### while trying to send to the boss, after which boss decides the below:
## rank 0 in job 35  gulabjamun.ncbs.res.in_56625 caused collective abort of all ranks
############ So ensure that NUMAVG+1 < 1000
####### For a network rather than isolated mitral cell, even 500 processes make the cluster hang.
####### Has worked only for 32 processes, didn't test inbetween yet.
##### Basically memory overflow problems - use less memory by using less data tables
NUMAVG = 50 # don't make NUMAVG higher than 200.

if IN_VIVO:
    #OBNet_file = '../netfiles/syn_conn_array_10000_singlesclubbed10_jointsclubbed1_numgloms1_seed'+netseedstr
    OBNet_file = '../netfiles/syn_conn_array_10000_singlesclubbed100_jointsclubbed1'\
        '_numgloms2_seed'+netseedstr+mitdistancestr
    granfilebase = "../firefiles/firefiles_baseline/firetimes_gran_baseline_noresp"
else:
    ## half the granules are lost in slicing :
    ## look at my old pre-CNS simulations with various r-dependent connectivity.
    ## even for columns, I assume half of the granules on the prim dend will die.
    ## Instead of half the number of syns, grans more than healthy_slice_width away in y are pruned.
    OBNet_file = '../netfiles/syn_conn_array_10000_singlesclubbed100_jointsclubbed1'\
        '_numgloms2_seed'+netseedstr+mitdistancestr
    granfilebase = "../firefiles/firefiles_baseline/firetimes_gran_baseline_invitro"
if DIRECTED:
    OBNet_file += '_directed'+str(FRAC_DIRECTED)
    if PROXIMAL_CONNECTION:
        OBNet_file += '_proximal'
    else:
        OBNet_file += '_distal'
if IN_VIVO: OBNet_file += '_2GLOMS.xml'
else: OBNet_file += '_2GLOMS_INVITRO.xml'

PLOT_EXTRAS = False # whether to plot the first few singles and joints for each data point.
if PLOT_EXTRAS: SPIKETABLE = False #make the mitral soma tables and SOME interneurons record Vm-s and not spiketimes.
else: SPIKETABLE = True #make the mitral soma tables and ALL interneurons record spiketimes and not Vm-s.

PG_raiseRMP = 0.0#7.5e-3 # 5mV
granule_raiseRMP = 0.0#7.5e-3 # 5mV
PG_inject = 0.0 #1e-12 # 1pA
granule_inject = 0.0 #1e-12 # 1pA

## unmodelled sister mitrals are not clubbed for activity dep inh 
## into modelled sister mitrals to multiply excitation to granules,
## as there is no common input via the glomerulus.
CLUB_MITRALS = False # If unmodeled sister mitrals connect to same granule as modeled sister mitrals, provide extra excitation to granule from modeled mitral
ONLY_TWO_MITS = True#False # Only two mitrals with indices (neuroml id-s) given in sim_utils.py to test lateral inhibition.

ODOR_GIVEN = False # No odor given only current injection as below
if IN_VIVO:
    onInject = 2000e-12 # current in B, roughly 70Hz firing w/o lateral - Actually Arevian et al 2008 use 60 to 100Hz in mitral B.
else:
    onInject = oninject_ext#1500e-12 # current in B, roughly 80Hz firing w/o lateral - Actually Arevian et al 2008 use 60 to 100Hz in mitral B.
if ASYM_TEST: Imax = 1001.0e-12#A # endpoint of activDDI plot
else: Imax = 2501e-12#3501.0e-12#3001.0e-12# A # endpoint of activDDI plot
ORNmax = 20.0

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