Research computing conducts first high-performance computing course for life sciences

May 29, 2018

Hunched over their laptops in University Hall, graduate students and post-doctoral fellows typed out commands in R code, following along with Michael Gribskov, professor of biological sciences at Purdue, to explore differential gene expression analysis.

The technique, new to the students, came with a kick: access to high-performance computing resources that would turn months of work into days.

The eight-week course, “HPC for Life Sciences,” was conceptualized by Gladys Andino, a senior scientific applications analyst with ITaP Research Computing; Nadia Atallah, a bioinformatician with the Purdue Center for Cancer Research; and Gribskov, who also holds a courtesy appointment in computer Science.

Gribskov says the class focuses on gene expression analysis because most of the students, though their research areas vary, are looking at some type of gene expression in their work.

“The expression of specific genes under different conditions or at developmental time points can be important in plant breeding, fruit size, or in treating animal diseases,” he says.

Andino, a recent recipient of the Internet2 Inclusivity Award, struggled with the initial dive into using high-performance computing for her research, too. Trained as an entomologist, she needed more robust methodologies to finish her doctoral work looking at Varroa mites’ transcriptome. She turned to bioinformatics and HPC, learning as she went with some programming courses to fall back on. Along the way, she met Gribskov and Atallah.

“Gibskov’s been a mentor to me and Atallah for a couple of years now,” Andino says. “We were all talking awhile back about whether we could or should teach a class, because in ITaP Research Computing we’d gotten so many requests for help that required more time than we had for our consulting sessions.”

The students in the course came with limited computational backgrounds. The three instructors had to design the course in a way that would provide fundamental math skills while also teaching basic computational code to help complete the students’ research.

Shaneka Lawson, an adjunct assistant professor in forestry and natural resources, says the skills she learned in the course are essential to her career development.

“Previously, I did everything the low-tech way and was losing so much time,” Lawson says. “I am deeply indebted to each of the instructors for sharing their knowledge with us.”

Atallah says life science students don’t always receive formal HPC training in their coursework. She pursued a certification in computational life sciences, but it is outside the norm to do so.

“The students gained a lot from those first lectures,” Atallah says. “Purdue is moving to include these types of classes into coursework, but in the meantime, there’s a gap.”

For the students of the first “HPC for Life Sciences” class, that gap was closed. “In spite of these students coming in with little-to-no background in HPC,” Gribskov says, “they were able to do cutting-edge HPC midway through the class.”

The three instructors say they would love to plan for another class and invite other colleagues to participate as well. Depending on the feedback, Andino says, there will likely be another eight-week course next spring semester.

To learn more about high-performance computing systems and consulting available from ITaP Research Computing, as well as research data storage and other services, contact Preston Smith, director of research services and support for ITaP, at 49-49729 or psmith@purdue.edu.

Originally posted: May 29, 2018  11:20am

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