Life science use of community clusters experiencing significant growth
Vikki Weake’s lab has its eyes on genes involved in sight — and sight’s deterioration with aging — research that might lead to new ways of prolonging the eyes’ lifespan.
“The eye is actually very accessible for treatment,” notes Weake, a Purdue assistant professor of biochemistry.
The research involves sorting through changes in tens of thousands of genes from aging fruit flies, the lab’s model organism, and millions of pieces of sequencing data from those genes. That’s done, in part, with complex statistical models developed by Weake’s collaborator Rebecca Doerge, Trent and Judith Anderson Distinguished Professor of Statistics.
“You’ve got to use very powerful computing,” Weake says.
Weake is one of a growing number of high-performance computing users from the life sciences on campus, particularly with the advent of the new Snyder cluster research supercomputer. From 2014 to 2015, nearly 100 new research groups began using Purdue’s Community Cluster Program supercomputers, the Research Data Depot data storage facility and related centralized resources from ITaP Research Computing. There were large increases in use by agriculture (54 percent), health and human sciences (57 percent) and biology (44 percent) along with new users in pharmacy and veterinary medicine.
ITaP built the Snyder cluster in 2015 at the same time it installed the new Rice cluster. While Rice is geared to physical sciences and engineering research, Snyder is designed for life sciences, including large memory capacity and an appropriate software array, among other things.
For information about Snyder, Rice, the Research Data Depot and other research computing systems and services email firstname.lastname@example.org or contact Preston Smith, ITaP’s director of research services and support, email@example.com or 49-49729.
Demand from faculty researchers has prompted ITaP Research Computing to expand Snyder three times already. Purdue’s Biochemistry Department purchased capacity in Snyder dedicated to use by its faculty.
“Everything we need is already in the cluster and ready to go,” says Whitney Dolan. A doctoral student in the lab of biochemistry Professor Clint Chapple, she’s studying ways to guide plant development at the level of genes and proteins, the better to tailor plants for use in biofuels, for example. Dolan also is a member of Purdue’s Computational Life Sciences Program.
Gladys Andino, a senior scientific applications analyst for ITaP Research Computing, focuses on assisting life science researchers at Purdue in using the community clusters and other research computing resources. She brings a valuable perspective to the job.
Her doctoral work under entomology Professor Greg Hunt, which involved a gene-level examination of virus-carrying mites that are in large part responsible for decimating honeybee populations, required the use of the clusters. Andino had no experience with high-performance computing. She tapped every resource she could on and off campus to learn how and honed her skills while applying what she learned to her research. When someone comes to her with a problem now, she can relate.
“I’ve been in that position when I really didn’t know what to do,” Andino says. “I know I would have appreciated someone taking me by the hand and telling me ‘here’s what you need to do.’”