Folders

Attenuation

For investigating the attenuation of the cell. Utilizes a -0.05 mA current clamp.

Creates the F-I curve for the cell. The reference current is 1.2 mA.

Looking at the cell’s input resistance.

This is where mechanisms and templates are stored. This folder is used as the basis for all simulations in the project.

mechanisms: where mod files are. pyr2pyr.mod and int2pyr.mod are the synapse mechanisms used.
morphologies: morphology files. cell1.asc is used.
synaptic_models: JSON files containing synaptic parameters. PN2PN.json and INT2PN.json are used.
templates: hoc cell templates. L5PCtemplate.hoc is the main template, and it utilizes L5PCbiophys3.hoc.

Warning

THIS NEEDS WORK

Where EPSC tuning is performed (on both basal and apical dendrites).

Warning

THIS NEEDS WORK

Confirming that our cell model matches the experimental firing properties that Hay et al. 2011 tuned for.

Where IPSC tuning is performed (perisomatic, basal, and apical).

Warning

THIS NEEDS WORK

Folder for exploring the morphology of the cell.

Folder for plotting the cell and synapse locations on the cell.

Used to build and check short term plasticity for both excitation and inhibition.

Used to ensure that a suprathreshold step current (0.793 mA) induces the proper behavior (as determined by Hay et al. 2011).