(Ching et al., 2010) TC, RE, and synaptic DynaSim mechanism files.
DynaSim-compatible mechanism files for simulation of the thalamus of (Ching et al., 2010).
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 thalamus from:
Ching, S., Cimenser, A., Purdon, P. L., Brown, E. N., & Kopell, N. J. (2010). Thalamocortical model for a propofol-induced alpha-rhythm associated with loss of consciousness. Proceedings of the National Academy of Sciences, 107(52), 22665–22670. http://doi.org/10.1073/pnas.1017069108
Note that this code diverges from the given equations due to typos and errors in the original equations. The code contained here has been ground-truthed and cross-checked across both the original code run for the paper and the source material that THAT code is based on, several times. In other words, the code contained here is more correct than the equations in the paper.
Install
The easiest way to get started with this is
- Install DynaSim
git cloneDynaSim to where you want to put the code- Add
addpath(genpath('/your/path/to/dynasim'))to your~/Documents/MATLAB/startup.mfile. Create the necessary folders and files if need be.
git clonethis repo into '/your/path/to/dynasim/models', i.e. the 'models' subdirectory of your copy of the DynaSim repo.- Set your own data directory inside the script, make your own changes, etc.
- Believe it or not...that should be it! You should be able to start MATLAB in any directory and run this script successfully! Let me know if there are problems, at austin.soplata 'at symbol' gmail 'dot' com
Note that there are extra synaptic mechanism files unused in the database that do things like simulate a persistent AMPAergic spike train down to the cells, etc., in order to mimic the cortex's input.