Code for generating Figures 3, 4, 5, & 7 of the following paper: Osinski & Kay (2016), Granule cell excitability regulates gamma and beta oscillations in a model of the olfactory bulb dendrodendritic microcircuit, J Neurophysiol. doi: 10.1152/jn.00988.2015 Code is designed to run in MATLAB R2015b Implementation is by Boleslaw Osinski , to whom questions should be addressed boleszek@uchicago.edu --------------------------------------------------------------------- The zipped folder includes the following .m files: InitNetwork_GCE.m - This function initializes network parameters OB_network_GCE.m - This is the numerical simulation of the Mitral-Granule network ILFP_GCE .m - This is a wrapper function for OB_netwrok_GCE.m. All simulation products as well as the simulated LFP are generated by this function ParamSweep_GCE.m - This is a wrapper function around ILFP_GCE.m. It evaluates the model for every combination of the two parameter inputs Rasterplot.m - Generates raster plot --------------------------------------------------------------------- Usage: 1. Unzip GCE_ModelDB.zip 2. Open MATLAB. Set MATLAB path to unzipped folder's directory. This can be done with MATLAB prompt commands like (where additional folders in the cd command may be necessary to find the new GCE_ModelDB folder) cd GCE_ModelDB addpath(pwd) 3. Open Fig3, Fig4, Fig5, or Fig7 directory and run the associated script (i.e. Fig3script.m) for producing the figures. Each folder includes it's own parameter file (i.e. OB_params_GCE_Fig3.txt) Notes: - Fig3script.m runs quickly and produces figures like those in the paper. I remade the figures for the Methods section (including Figure 3) at the very beginning of the revision process, and there were subsequent minor changes to the final model (such as adjusting changing the proportionality between Ca concentration and N-type current and [Ca] threshold for GABA release). The slightly different trajectories in Figure 3 resulting from these changes do not change the network behavior of the model.: Fig 3 A Fig 3 B Fig 3 C Fig 3 D - Fig4script.m runs for ~ 4min Fig4script.m uses the tightfig function which can be found at the MATLAB file exchange at http://www.mathworks.com/matlabcentral/fileexchange/34055-tightfig Fig 4 A.i - Fig5script.m runs for ~ 3.5hr - Fig5script.m uses the shadedErrorBar function which can be found at the MATLAB file exchange at http://www.mathworks.com/matlabcentral/fileexchange/26311-shadederrorbar and the coherencycpt function from the Chronux toolbox (Version 2.11) which can be downloaded at http://chronux.org - Fig7script.m runs for ~ 1.5hr