Publications

Table of Contents:

• Papers
• Posters
• Talks
• Resources
• Software

Papers

• Soplata, Austin E., Michelle M. McCarthy, Elie M. Adam, Patrick L. Purdon, Emery N. Brown, and Nancy Kopell. Neuromodulation Due to Propofol Affects Anesthetic Oscillatory Coupling. bioRxiv, February 20, 2022. https://doi.org/10.1101/2022.02.17.480766
  • Local PDF download here.
  • Code: The reproducible code for this paper’s simulations are available in this GitHub repo.
  • Code: If you only want the model equation code, that is available in this GitHub repo.
• 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
  • Local PDF download here.
  • Code: The reproducible code for this paper’s DynaSim and Brian2 benchmarks is available here in this repo.
• 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
  • Local PDF download here.
  • Code: The reproducible code for this paper is available both here as a standalone repo or here in “plugin” form for use with DynaSim, available here.

Posters

• SFN 2019: A. SOPLATA; M. MCCARTHY; E. ROBERTS; E. BROWN; P. PURDON; N. KOPELL. Cortical UP DOWN state synchrony drives propofol phase amplitude coupling in slow waves. Program No. 289.18. Neuroscience 2019 Abstracts. Chicago, IL: Society for Neuroscience, 2019. Online.

• SFN 2016: A. SOPLATA; J. SHERFEY; E. BROWN; P. PURDON; N. KOPELL. Thalamic generation of propofol phase amplitude coupling. Program No. 507.13. Neuroscience 2016 Abstracts. San Diego, CA: Society for Neuroscience, 2016. Online.

  • To see the actual source code for this poster, go to the GitHub repo here.

Talks

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

• 2021-03-10 “Dynamics of propofol anesthesia in the thalamocortical loop” Thalamus Trainees Meeting Group
• 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 for the Computational Neuroscience Students Organization
• 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. https://doi.org/10.1016/j.cub.2016.08.035

Resources

• I maintain collaborative, public lists of:
  • Open Computational Neuroscience Resources
  • Open Science Resources

Software

• 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.