# Hippocampal CA3 model (Sherif et al, 2020) This is the code for the CA3 hippocampal model in the paper by [Sherif et al](https://www.nature.com/articles/s41537-020-00109-0), 2020, in npj Schizophrenia. The code has been updated to use Python3. In addition to [NEURON](https://neuron.yale.edu/neuron/), the following python packages are needed: hyp5 configparser (You can use conda or pip to install them). After you install the required packages, compile the mod files: nrnivmodl To plot a figure similar to figure 1 in the paper with the control conditions, you will need first to run a control simulation. The configuraiton file with the parameters for the model are in fig1simulationConfig.cfg file. The following code will run a simulation that is 3 seconds long (it takes around one minute to run on my machine with 8 cores), and save the resulting output file in directory ./data/batch. After the file has been generated (or if you want to plot the provided output sample file), you can run the following code: python -i analysisPlottingCode.py Then inside python: simstr = 'controlSimulation' # name of simulation that just ran - set in the configuration file. loadedSim = loadSimH5py(simstr, datadir = './data/batch/') myfig, rastsp, lfpsp, psdsp = plotloadedsimProfiling(loadedSim, 0) rastsp.set_xlim(2000, 3000) # plot the last 1000 ms (1 second). # annotate y-axis of raster for the different neuronal populations rastsp.set_ylabel('') rastsp.set_yticklabels('') rastsp.annotate('PYR', xy=(-0.1, 0.33), xycoords='axes fraction', color = 'red', fontsize = 12, fontweight='bold') rastsp.annotate('PV', xy=(-0.1, 0.73), xycoords='axes fraction', color = 'green', fontsize = 12, fontweight='bold') rastsp.annotate('OLM', xy=(-0.1, 0.88), xycoords='axes fraction', color = 'blue', fontsize = 12, fontweight='bold') # change color of LFP voltage plot to black lfpline = lfpsp.get_lines()[0] lfpline.set_color('k') # change color of PSD plot to black psdline = psdsp.get_lines()[0] psdline.set_color('k') You should get a figure similar to the one below: ![Alt text](/getmodelfile?model=258738&file=CA3modelCode_npjSchizophrenia_September2020--main/fig1sample.png?raw=true "Optional Title") Changelog --------- 2022-12: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON.