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README.md

(Soplata et al., 2017) TC, RE, and synaptic DynaSim full simulation reproduction files.

This contains the complete DynaSim code files (in dynasim), model mechanism files (in models/personal/propofol-coupling-2017-mechanisms), and simulation runscripts (in runscripts) needed for simulation of the thalamus of (Soplata et al., 2017), inherited from (Ching et al., 2010). Note that you should NOT run these scripts unless you have access to a parallel computing cluster that DynaSim integrates with (and all the MATLAB licenses that that entails)! The main batch of these involve almost 10,000 simulations of ~100 relatively complex cells (and their combinatorial synaptic connections) for almost 10 seconds at a high fixed-step resolution (Euler, 0.01 ms), and each individual simulation creates over 1GB of data! All simulations were set to run with a default memory/RAM allowance of 256GB. You will NOT be able to run all these simulations on your personal computer in a reasonable amount of time, unless you are a time traveler from the year 2054.

Adding the dynasim directory and all its subdirectories to your MATLAB path should enable you to run all the simulations for the computational thalamus from:

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

This model was inherited 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 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).

Also note that, while this will create all of the subplots used in the figures in the paper INDIVIDUALLY, the subplots were reformatted in Inkscape by hand. No data or coloration was changed, and axis tick values were replaced with the same values, but formatted differently to look better and for a more consistent style.

Original reproduction

These mechanism files are approximately as they were used originally, which means this copy of DynaSim is using commit 4a20467; however, the version used for each batch of simulation may have varied, and so feel free to contact me if there are any errors preventing simulations from running from scratch.

If you want just the mechanism files alone, go to propofol-coupling-2017-mechanisms.

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Complete DynaSim code for reproduction of (Soplata et al., 2017)

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