I serve as the Research Computing Center (RCC) computational scientist dedicated to COLSA, facilitating research via the following services:
Bioinformatics, HPC, and other scientific application development and support
GEN 712/812, teaching Bash and Python programming to students in the life sciences
Coordination of RCC managed COLSA technology, including compute, storage, and high-capacity data transfer resources
Assistance incorporating RCC managed resources into grant proposals and other documentation
Assistance organizing computational pipelines, workflows, and data management practices for increased usability and efficiency
Development and support of the PALADIN protein alignment application and associated tools
Experience with a range of applications, including Slurm, BWA, MAKER, Spades, ImageJ/FIJI, and many other packages (see here)
Please don’t hesitate to reach out if I can be of any assistance in these areas!
My academic interests lie across a few areas, including metagenomic characterization, modeling biological systems, image processing, graphics, visualization, HPC, and generally any tricky problems that can be solved with a computer. Off hours, I enjoy gaming (video, board, card), FPGA design, retrocomputing, ancient history, and large amounts of Camellia sinensis. Feel free to stop by my office to chat about any of these topics and more!
B.S., Computer Science, University of New Hampshire
Westbrook, A., Varki, E., & Thomas, W. K. (2021). RepeatFS: a file system providing reproducibility through provenance and automation. BIOINFORMATICS, 37(9), 1292-1296. doi:10.1093/bioinformatics/btaa950
Park, C. J., Macartney, K. J., Shen, J., Xie, K., Zhang, X., Bergeron, R. D., . . . ACM. (2018). A Novel Approach for Increasing Taxonomic Resolution in Protein-Based Alignments. In ACM-BCB'18: PROCEEDINGS OF THE 2018 ACM INTERNATIONAL CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY, AND HEALTH INFORMATICS (pp. 538). doi:10.1145/3233547.3233646
Schuelke, T. A., Wu, G., Westbrook, A., Woeste, K., Plachetzki, D. C., Broders, K., & MacManes, M. D. (2017). Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia. GENOME BIOLOGY AND EVOLUTION, 9(12), 3312-3327. doi:10.1093/gbe/evx242
Westbrook, A., Ramsdell, J., Schuelke, T., Normington, L., Bergeron, R. D., Thomas, W. K., & MacManes, M. D. (2017). PALADIN: protein alignment for functional profiling whole metagenome shotgun data. BIOINFORMATICS, 33(10), 1473-1478. doi:10.1093/bioinformatics/btx021
Aggarwal, T., Westbrook, A., Broders, K., Woeste, K., & MacManes, M. D. (2016). De novo Genome Assembly of Geosmithia morbida, the Causal Agent of Thousand Cankers Disease. doi:10.1101/036285