DynaSim mechanism files for simulating (Bazhenov et al., 2002)

DynaSim-compatible mechanism files for simulation of the cortex and thalamus of (Bazhenov et al., 2002).

Adding these mechanism files and associated functions into where you keep your mechanism files for DynaSim, e.g. /your/path/to/dynasim/models, should enable you to simulate the computational cortex and thalamus from:

Bazhenov M, Timofeev I, Steriade M, Sejnowski TJ. Model of thalamocortical
slow-wave sleep oscillations and transitions to activated states. The
Journal of Neuroscience. 2002;22: 8691–8704.

The original code for the (Bazhenov et al., 2002) model can be found here at ModelDB. Note that this is only intended to reproduce the qualitative behavior of the "base", not the "extended" model of the paper. That said, there are experimental adjustment factors in the code that would make modeling the extended model easy. Also note that this is NOT intended as a bit-perfect reproduction of the original model, but rather just an open-source, adequate reproduction of the overall qualitative results.

NOTE: This must be run using a custom version of DynaSim (see below) and has only been tested for MATLAB 2017a. Let me know if you want to run it and I'll help!

Install and Usage

The easiest way to get started with this is:

1. Install this custom version of DynaSim (https://github.com/asoplata/DynaSim/tree/coupling_addition), including adding it to your MATLAB path.
2. git clone or download this code's repo (https://github.com/asoplata/dynasim-bazhenov-2002-model) into '/your/path/to/dynasim/models', i.e. the 'models' subdirectory of your copy of the DynaSim repo.
3. Start MATLAB, and run the main runscript runBazhenovModel.m.

References

1. Bazhenov M, Timofeev I, Steriade M, Sejnowski TJ. Model of thalamocortical slow-wave sleep oscillations and transitions to activated states. The Journal of Neuroscience. 2002;22: 8691–8704.