DynaSim mechanism files for simulating thalamically-extended (Benita et al., 2012) Slow Wave model

DynaSim-compatible mechanism files for simulation of a new, hybrid model consisting of the cortex of (Benita et al., 2012), the thalamus of (Soplata et al., 2017), and simple AMPAergic thalamocortical and corticothalamic connections.

This is NOT intended as a bit-perfect reproduction of any original model, but rather just an open-source, adequate reproduction of the overall qualitative results of the individual models.

This was last run using Matlab 2022a and this commit of DynaSim: https://github.com/DynaSim/DynaSim/commit/b1aa46d29bd96a4383f5831211fbae73a0ff709f .

Install and Usage

The easiest way to get started with this is:

1. Install the "dev" branch of DynaSim (https://github.com/DynaSim/DynaSim/wiki/Installation), including adding it to your MATLAB path.
2. Run git clone https://github.com/asoplata/dynasim-extended-benita-model or download this code's repo (https://github.com/asoplata/dynasim-extended-benita-model) manually into <YOUR_DYNASIM_INSTALL_FOLDER>/models/personal, which you may have to create if it doesn't exist.
3. This is meant to be used in conjunction with the runscripts in https://github.com/asoplata/soplata-2023-thalcort-code .

References

1. Benita, J. M., Guillamon, A., Deco, G., & Sanchez-Vives, M. V. (2012). Synaptic depression and slow oscillatory activity in a biophysical network model of the cerebral cortex. Frontiers in Computational Neuroscience, 6. https://doi.org/10.3389/fncom.2012.00064
2. Soplata AE, McCarthy MM, Sherfey J, Lee S, Purdon PL, Brown EN, et al. (2017) Thalamocortical control of propofol phase-amplitude coupling. PLoS Comput Biol 13(12): e1005879. https://doi.org/10.1371/journal.pcbi.1005879