README

This is the readme for code in support of the paper:

Front Hum Neurosci. 2010 Nov 22;4:198. Computational modeling of
distinct neocortical oscillations driven by cell-type selective
optogenetic drive: separable resonant circuits controlled by
low-threshold spiking and fast-spiking interneurons. Vierling-Claassen
D, Cardin JA, Moore CI, Jones SR.

Code was generated using NEURON Version 6.1

Primary author of code was Dorea Vierling-Claassen (contact at
dorea@brown.edu), in consultation with Mike Sikora, based on previous
models by Stephanie R. Jones (2007 and 2009, also available on Model
DB)

TO RUN:

Compile folder using mknrndll, then run the file light_batch_FSdrive,
which generates 11 separate files, each containing 600 ms simulation,
for baseline and 10 drive frequencies in the modeled case of light
drive to fast-spiking (FS) cells case (files are saved in folder
titled "batchsims")

FILE INFORMATION:

lightgamma_init_DB.hoc is called by light_batch_FSdrive and loads all
relevant processes from the following files:

1) lightgamma_network_DB.hoc defines cell morphology, intrinsic
currents and synaptic dynamics for each cell type

2) lightgamma_wiring_DB.hoc contains processes for wiring between
populations and depends on files controlling random connectivity in
confiles folder, connectivity is fixed for all runs. Connectivity
files were generated in matlab using light_genconn_DB.m, also
included. Connectivity files included here are exactly as in the
published work.

3) lightgamma_wiring_proc_DB.hoc includes processes for light drive

4) lightgamma_localconn_DB.hoc sets network connectivity

5) lightgamma_drive_DB.hoc sets light drive to either FS or RS cells,
to run the RS case, will need to comment out FS drive and comment in
RS drive in this file

6) lightgamma_noise_DB.hoc adds background noise, based on a
modification of noise from Destexhe et al 2001, also available on
model DB

7) lightgamma_LFP_DB.hoc contains process to generate average voltage
over all pyramidal cells, which was the bases for subsequent signal
processing

** This code runs the FS case, to run the case of RS drive, define new
filenames in light_batch_FS, comment out the FS drive and comment in
the RS drive in lightgamma_drive_DB**

Many thanks to other contributers to model DB's whose .mod files are
included here. Credits are in individual files and additional
citations are in the published work.

-----
Last updated 9-22-2011, Dorea V-C

Changelog
=========

* 20220924: Update MOD files to avoid declaring variables and functions with the same name.
  See https://github.com/neuronsimulator/nrn/pull/1992