# 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: [guoshi_li@med.unc.edu](mailto:guoshi_li@med.unc.edu) --- ## 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")