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.