DynaSim mechanism files for reproduction of (Soplata et al., 2017)
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models
testing
README.md
tcre_run_script.m

README.md

(Soplata et al., 2017) TC, RE, and synaptic DynaSim mechanism files.

DynaSim-compatible mechanism files for simulation of the thalamus of (Soplata et al., 2017), inherited from (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 this paper:

Soplata AE, McCarthy MM, Sherfey J, Lee S, Purdon PL, Brown EN, et al.
Thalamocortical control of propofol phase-amplitude coupling. PLOS
Computational Biology. 2017;13: e1005879. doi:10.1371/journal.pcbi.1005879

This model was inherited from this paper:

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 of (Ching et al., 2010) 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, used in (Soplata et al., 2017), is more correct than the equations in the Supplementary Information of (Ching et al., 2010).

Install

The easiest way to get started with this is

  1. Install DynaSim (see here for instructions)
  2. git clone this repo into '/your/path/to/dynasim/models', i.e. the 'models' subdirectory of your copy of the DynaSim repo.
  3. Set your own data directory inside the sample runscript tcre_run_script.m, make your own changes, etc.
  4. 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, unused synaptic mechanism files that do things like simulate a persistent AMPAergic spike train down to the cells, etc., in order to mimic the cortex's input.

Original reproduction

These mechanism files are AS THEY WERE USED originally, which means they were used under a version of DynaSim likely using the following commit: 4a20467

If you want a COMPLETE installation to reproduce the simulations used in the paper, go to propofol-coupling-2017-full.