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, parameter sweeping, and plug-and-play functionality. The primary author is Dr. Jason Sherfey, and other contributors include Erik Roberts, Dr. Dave Stanley, Dr. Salva Ardid, and Dr. Ben Polletta.
  • 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 that match a bash match (including wildcards) and builds a single HTML file with references to the PNGs, allowing for quick 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  • evernote-to-markdown, a very preliminary, possibly out of date program to convert Evernote XML files into Markdown files.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.