This model corresponds to the paper: "Basal tree complexity shapes functional pathways in the prefrontal cortex", Papoutsi et al., 2017 The code was written in NEURON version 7.3 Model usage: Download and expand the archive and compile the mod files located in the "mod_files" folder. In the simulation folder: "network_coincidence.hoc" sets up the simulation parameters and runs the model. "L5PFC_biophysics.hoc" defines the biophysical properties of pyramidal neurons. "incell.hoc" defines the biophysical properties of the fast-spiking interneuron. "microcircuit.hoc" includes the procedures for connecting neurons. "background_noise.hoc" includes the procedures for spontaneous activity. "time_stim.hoc" includes procedures for activating the pyramidal neurons. To generate the data corresponding to Figure 7 of Papoutsi et al., 2017, run run_network_time.sh Specifically, simulation parameters are: cl_id (1,2): Select the cluster (corresponding to different morphologies of the basal tree) to simulate. interval_t: the inter-stimulus interval of the two events. num_run: the number of repetitions. Parameters are for the scaled condition of the biophysical properties of neurons with their original morphologies. For the uniform condition set "SCALED" parameter in L5PFC_biophysics.hoc to 0 and for the modified morphologies (same soma and apical tree, different basal trees) modify the basepath in L5PFC_biophysics.hoc: manipulation="modified". 20170726: To simulate an instance of the model run mosinit.hoc, which runs the simulation once with a particular choice of parameters to demonstrate the model running. For more help on running see: https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml When the model starts click on the "run simulation" button, then after a couple minutes you will see graphs like the one on the right: The graph on the left was created in the NEURON GUI by selecting Graph -> Shape plot.