Valerie Daggett has been utilizing U.S. National Science Foundation (NSF) ACCESS allocations on Expanse at the San Diego Supercomputer Center (SDSC), part of the UC San Diego School of Computing, Information and Data Sciences (SCIDS), to teach University of Washington (UW) students how to use supercomputers for their bioengineering research endeavors.
As a professor in the Department of Bioengineering in UW’s School of Medicine and College of Engineering, Daggett has specifically been using the supercomputer to teach a computational protein design course to both undergraduate and graduate students.
“We are using our ACCESS allocations to teach computational design and protein engineering methods from the lens of biomedical applications along with current research within the field,” Daggett said. “Specific topics in our course and lab work include molecular visualization, homology modeling, molecular dynamics simulations, computational protein design and design evaluations.”
Thanks to U.S. National Science Foundation ACCESS allocations, we are able to teach both undergraduate and graduate students how to utilize high-performance computing.
–Valerie Daggett, bioengineering professor in UW’s School of Medicine and College of Engineering
She said that the first half of the course allows students to apply computational design and protein engineering methods to a defined problem through guided weekly labs while the second half of the course allows them to choose their own problem and again apply the learned computational methods.
“Without access to SDSC’s Expanse, we would not be able to expose these students to high-performance computing,” Daggett said. “This past quarter we had more than 20 students in our class and we anticipate that many or more for each upcoming quarter.”
Resource Provider Institution(s): San Diego Supercomputer Center (SDSC)
Affiliations: University of Washington
Funding Agency: NSF
Grant or Allocation Number(s): BIO230224
The science story featured here was enabled by the U.S. National Science Foundation’s ACCESS program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.