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portfolio

pplacerDC

A divide and conquer method for placing query sequences in large phylogenetic trees.

TSGL

The Thread Safe Graphics Library is designed for CS education. My work includes creating visualizations to demonstrate classic synchronization problems taught in OS courses in order to enable students to learn more visually.

publications

TSGL: A tool for visualizing multithreaded behavior

Published in SIGCSE '19: Proceedings of the 50th ACM Technical Symposium on Computer Science Education, 2018

This paper describes the thread safe graphics library (TSGL), a tool by which an educator can add graphics calls to a working multithreaded program in order to make visible the underlying parallel behavior.

Recommended citation: Joel C. Adams, Patrick A. Crain, Christopher P. Dilley, Christiaan D. Hazlett, Elizabeth R. Koning, Serita M. Nelesen, Javin B. Unger, Mark B. Vande Stel, 'TSGL: A tool for visualizing multithreaded behavior,' Journal of Parallel and Distributed Computing, Volume 118, Part 1, 2018, Pages 233-246, ISSN 0743-7315, https://doi.org/10.1016/j.jpdc.2018.02.025. http://academicpages.github.io/files/TSGL.pdf

pplacerDC: a new scalable phylogenetic placement method

Published in BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2021

pplacerDC uses a divide and conquer approach with pplacer in order to more scalably place queries in phylogenetic trees

Recommended citation: Elizabeth Koning, Malachi Phillips, and Tandy Warnow. 2021. pplacerDC: aNew Scalable Phylogenetic Placement Method. In 12th ACM InternationalConference on Bioinformatics, Computational Biology and Health Informatics(BCB '21), August 1-4, 2021, Gainesville, FL, USA. ACM, New York, NY, USA,9 pages. https://doi.org/10.1145/3459930.3469516 https://dl.acm.org/doi/10.1145/3459930.3469516

talks