Anthony Westbrook

Anthony Westbrook

Office: Student Postal Center, Payroll Office, Durham, NH 03824

My Role at UNH

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!

Resources

I maintain PALADIN, the UNH SDB ParaView plugin, and a variety of other software in my Github repository: https://github.com/twestbrookunh

Discover all the services the UNH RCC provides:  http://www.unh.edu/research/support-units/research-computing-center

Information on the Premise HPC cluster can be found here: http://premise.sr.unh.edu/

Contact Me

Office: 436 Gregg Hall

Email: anthony.westbrook@unh.edu

LinkedIn: Toni Westbrook

Twitter: @ToniWestbrook

Courses Taught

  • GEN 712/812: Programming for Bioinformatics
  • MCBS 913: Applied Bioinformatics

Education

  • B.S., Computer Science, University of New Hampshire

Research Interests

  • Bioinformatics
  • Computer Science
  • Genomics

Selected Publications

  • 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

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  • Most Cited Publications