Table of Contents:
- 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.
- Sherfey JS, Soplata AE, Ardid S, Roberts EA, Stanley DA, Pittman-Polletta BR, et al. DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation. Front Neuroinform. 2018;12. doi:10.3389/fninf.2018.00010
To see the actual source code for these talks, go to the GitHub repo
- 2018-04-23 Monday, “Thalamic Control of Propofol Phase-amplitude Coupling”
Cognitive Rhythms Collaborative Retreat, MIT,
- 2017-11-17 Friday, Git Introduction for BU CNSO, Boston University,
going over both the basics of
Git and how to contribute to the BU-CNSO website repo on
- 2016-10-13 Thursday, NaK Group talk, Boston University,
reviewing this paper:
Niethard, N., Hasegawa, M., Itokazu, T., Oyanedel, C. N., Born, J., & Sato,
T. R. (2016). Sleep-Stage-Specific Regulation of Cortical Excitation and
Inhibition. Current Biology.
- I maintain public lists of:
- 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
- Here is a working DynaSim
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.
- 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
- 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very preliminary, possibly out of date program to convert Evernote XML files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.