NEURON Code for Implementing 2D Olfactory Bulb (OB) Model of Gamma Oscillations

Author:
Guoshi Li
Department of Psychiatry
University of North Carolina at Chapel Hill
Chapel Hill, NC 27599

Reference:
Li G and Cleland TA (2017). A coupled-oscillator model of olfactory bulb gamma oscillations. PLoS computational biology, 13(11), e1005760.

For questions, please email: [email protected]

---

Overview

The OB model is implemented with NEURON 7.3, and simulations are run under both CentOS Linux and Ubuntu Linux.

The default OB network model contains:

• 25 mitral cells (MCs)
• 25 periglomerular cells (PGs)
• 100 granule cells (GCs)

Package Contents

The package contains the following folders:

• celldata: Stores data from single-cell simulations
• data0: Stores data from network simulations
• connection: Stores connectivity information between MCs and GCs
• Input: Stores odor input values
• Readme: Contains model information

Running Simulations

• Network simulation: Run mosinit.hoc
• MC single-cell simulation: Run MC_Stim.hoc
• GC single-cell simulation: Run GC_Stim.hoc
• PG single-cell simulation: Run PG_Stim.hoc

Major HOC Files

• Parameter.hoc: Specifies the parameters of the OB model
• Connect.hoc: Specifies network connectivity
• Background.hoc: Generates random background inputs to the network
• Input.hoc: Generates odor inputs to the network
• Figure.hoc: Generates graphic displays of network simulation results (optional)
• SaveData.hoc: Saves all relevant data into files for later analysis

---

Simulation Details

• Simulation step: 0.002 ms
• Default simulation time: 3000 ms (3 seconds)

---

Data Analysis

The data saved in the data0 folder after simulation can be analyzed using the following custom MATLAB scripts.
Note: The simulation time must be 3000 ms (3 seconds) for the MATLAB scripts to run properly.

• PlotV.m: Plots cell membrane voltages
• Pro_Delay.m: Plots spike propagation delay of one representative MC
• PlotG.m: Plots GABAa conductances
• Rasterplot.m: Generates raster plots of spikes
• LFP.m: Performs frequency analysis of the simulated local field potential (sLFP)
• Load_data.m: Loads all relevant data into the workspace (to save the data into a .mat file for future analysis)

---

Changelog

• 2022-05: Updated MOD files to compile with the latest NEURON releases where ion variables used as STATE cannot be declared as GLOBAL.
• 2025-04-06: Reformatted readme. Removed backup files and __MACOSX folder. Added full reference information (was previously listed as "in press")