2D model of olfactory bulb gamma oscillations (Li and Cleland 2017)

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Accession:232097
This is a biophysical model of the olfactory bulb (OB) that contains three types of neurons: mitral cells, granule cells and periglomerular cells. The model is used to study the cellular and synaptic mechanisms of OB gamma oscillations. We concluded that OB gamma oscillations can be best modeled by the coupled oscillator architecture termed pyramidal resonance inhibition network gamma (PRING).
Reference:
1 . Li G, Cleland TA (2017) A coupled-oscillator model of olfactory bulb gamma oscillations PLOS Computational Biology, in press
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Olfactory bulb main mitral cell; Olfactory bulb main interneuron granule MC cell; Olfactory bulb main interneuron periglomerular cell;
Channel(s):
Gap Junctions:
Receptor(s): AMPA; NMDA; GabaA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s):
Implementer(s): Li, Guoshi [guoshi_li at med.unc.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral cell; Olfactory bulb main interneuron periglomerular cell; Olfactory bulb main interneuron granule MC cell; GabaA; AMPA; NMDA;
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OBGAMMA
celldata
connection
data0
input
README
cadecay.mod *
cadecay2.mod *
Caint.mod *
Can.mod *
CaPN.mod *
CaT.mod *
GradeAMPA.mod *
GradeGABA.mod *
GradNMDA.mod *
hpg.mod *
kAmt.mod *
KCa.mod *
KDRmt.mod *
kfasttab.mod *
kM.mod *
KS.mod
kslowtab.mod *
LCa.mod *
nafast.mod *
NaP.mod *
Naxn.mod *
Nicotin.mod *
nmdanet.mod *
OdorInput.mod *
SineInput.mod
Background.hoc
Cal_Synch.hoc
Connect.hoc
Figure.hoc
GC_def.hoc
GC_save.hoc *
GC_Stim.hoc
Input.hoc
mathslib.hoc
MC_def.hoc
MC_save.hoc
MC_Stim.hoc
mosinit.hoc
OBNet.hoc
Parameter.hoc
PG_def.hoc
PG_save.hoc *
PG_Stim.hoc
SaveData.hoc
tabchannels.dat *
tabchannels.hoc
                            
 
//===============================================================================================================   
	NEURON CODE FOR IMPLEMENTING 2D OLFACTORY BULB (OB) MODEL OF GAMMA OSCILLATIONS

				Guoshi Li
                                Department of Psychiatry
				Univeristy of North Carolina at Chapel Hill
                                Chapel Hill, NC 27599

A full description of the model may be found in:
Li G and Cleland TA (2017) A coupled-oscillator model of olfacotry bulb gamma oscillations. 
PLOS Computational Biology (In press).


For questions, please email: guoshi_li@med.unc.edu
											
//==================================================================================================================

Then OB model is implemented with NEURON 7.3 and simulation is run under both CentOS Linux and Ubuntu Linux. 
	
The default OB network model contains 25 mitral cells (MCs), 25 periglomerular cells (PGs) and 100 granule cell (GCs)
 
The package contains five folders:
"celldata" folder to store data from single cell simulations
"data0" folder to store data from network simulations 
"connection" folder to store the connectivity information between MCs and GCs
"Input" folder stores odor input values
"Readme" folder has model information

For network simulation, run mosinit.hoc
For MC single-cell simulation, run MC_Stim.hoc
For GC single-cell simulation, run GC_Stim.hoc
For PG single-cell simulation, run PG_Stim.hoc

Other major hoc files are described as follows:

Parameter.hoc: Specify the parameters of the OB model
Connect.hoc: Specify network connectivity 
Background.hoc: Generate random background inputs to the network
Input.hoc: Generate odor inputs to the network
Figure.hoc: Generate graphic display of the network simulation results (Optional)
SaveData.hoc: Save all relevant data into files for later analysis


The simulation step is set to 0.002 ms and the default simulation time is 3000 ms (3 sec) 


The data saved in the "data0" folder after simulation can be analyzed using the following custom Matalb scripts.
The simulation time needs to be 3000 ms (3 sec) for the m-files to run properly!

PlotV.m: plot cell membrane voltages
Pro_Delay.m: plot spike propogation delay of one representative MC
PlotG.m: plot GABAa conductances
Rasterplot.m: generate raster plots of spikes
LFP.m:   frequency analysis of the simulated local field potential (sLFP)
Load_data.m: Load all relevant data into the workspace (in order to save the data into a mat file for future analysis)
 





 



Li G, Cleland TA (2017) A coupled-oscillator model of olfactory bulb gamma oscillations PLOS Computational Biology, in press

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