Published in Bioinformatics Advances, 2025
This paper describes Poplar, a tool for parallelizing a phylogenomic pipeline.
Recommended citation: Elizabeth Koning, Arjun Subedi, Raga Krishnakumar, Poplar: A Phylogenomic Pipeline, Bioinformatics Advances, 2025;, vbaf104, https://doi.org/10.1093/bioadv/vbaf104 https://doi.org/10.1093/bioadv/vbaf104
Published in 2024 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2024
This paper describes the NothingModel, a proposed model for benchmarking systems that run Agent Based Models.
Recommended citation: Elizabeth Koing, William Gropp, 'Proposal for a Flexible Benchmark for Agent Based Models,' 2024 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Volume 118, Part 1, 2024, Pages 835-838, ISSN 979-8-3503-6460-6, https://doi.org/10.1109/IPDPSW63119.2024.00149 http://kodingkoning.github.io/files/ParSocial24_Benchmark_Proposal.pdf
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
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://kodingkoning.github.io/files/TSGL.pdf