Æsop Austin E Soplata


Table of Contents:




To see the actual source code for these talks, go to the GitHub repo here.



  • I try to make all the code/data for my publications as reproducible as possible. For code specific to each paper, see above.
  • I’ve contributed to DynaSim, a very powerful ODE solver system written in MATLAB with built-in parallelization, cluster support, grid-search parameter sweeping, and plug-and-play mechanism functionality. The primary author is Dr. Jason Sherfey, and other contributors include Drs. Erik Roberts, Dave Stanley, Salva Ardid, and Ben Polletta.
  • Here is a working DynaSim implementation for a connected combination of the cortical model of the first paper and thalamic model of the second paper here:

    Benita, Jose M., Antoni Guillamon, Gustavo Deco, and Maria V. Sanchez-Vives. “Synaptic Depression and Slow Oscillatory Activity in a Biophysical Network Model of the Cerebral Cortex.” Frontiers in Computational Neuroscience 6 (2012). https://doi.org/10.3389/fncom.2012.00064

    Destexhe, Alain, Thierry Bal, David A. McCormick, and Terrence J. Sejnowski. “Ionic Mechanisms Underlying Synchronized Oscillations and Propagating Waves in a Model of Ferret Thalamic Slices.” Journal of Neurophysiology 76, no. 3 (1996): 2049–70. https://doi.org/10.1152/jn.1996.76.3.2049

  • Here is a working DynaSim implementation for the thalamocortical model of the following paper:

    Krishnan GP, Chauvette S, Shamie I, Soltani S, Timofeev I, Cash SS, et al. Cellular and neurochemical basis of sleep stages in the thalamocortical network. eLife. 2016;5: e18607. https://doi.org/10.7554/eLife.18607

  • ya-pandoc-template, a simple system (wrapper) combining a Makefile with Pandoc templates that lets you effortlessly turn Markdown content into HTML presentations, LaTeX documents, etc. using personally-stylized templates.
  • poorquery, a program for quickly visualizing a large number of PNG picture files. This finds all PNG files with filenames that match a sed regular expression and then builds a single HTML file with references to the PNGs, allowing for quick, controllable, and “sliceable” viewing of very many PNGs in your browser.
  • evernote-to-markdown, a very preliminary, possibly out of date program to convert Evernote XML files into Markdown files. In the future I’ll probably make something like this for Evernote -> Emacs’ Org mode.
  • A collection of simple bash scripts I find to be particularly helpful when searching across code and interacting/synchronizing files between my local computer and a cluster.