Community clusters drive food science research, education at Purdue
August 22, 2017
Stephen Lindemann learned cutting-edge computational biology techniques as a Purdue undergraduate and honed those skills in his graduate and postdoctoral research. Now that he’s back on campus as an assistant professor of Food Science and Nutrition Science, he wants to pass those tools onto the next generation. It was this goal that led him to offer a course on microbial genomics using ITaP’s Scholar cluster.
“More and more, genomics is central to understanding the function of microbial communities. It’s been really important in my own research,” says Lindemann. “I’ve noticed there’s a certain amount of trepidation in dealing with computational biology, so one of the major goals of this class was to simply demystify the process and say, ‘Yes, you can do this, and it can be useful for your research.’”
Because many of the students in the class had no previous experience with high-performance computing, they began by learning basic UNIX commands and how to submit jobs to Purdue’s community clusters, in a series of classes taught by Gladys Andino, ITaP senior scientific applications analyst. The students then used Scholar’s bioinformatics tools to assemble genomes and annotate them to predict the genes’ functions.
Eventually, the students analyzed an entire bacterial genus, Roseburia, which lives in the colon and produces chemicals that may play a role in protecting the body against colon cancer. Each of the students processed the genome of a particular species, and they performed comparative genomics across the different species, making predictions about which species could perform certain functions. They are currently combining their individual papers into one large submission to the journal Microbial Genomics.
Jack Burnett, a graduate student in food science, studies the presence and persistence of Listeria and Salmonella bacteria in grocery stores. To determine if the strain is persistent or not, he needed to learn how to perform whole genome sequence analysis, which motivated him to sign up for Lindemann’s microbial genomics course.
“I will absolutely use what I learned in my own research going forward,” says Burnett, who has already taught genome annotation techniques to some of the students in his lab. “Now that I have these tools, there’s a lot of information I can find out about these strains of bacteria in a short period of time.”
While he uses Scholar in the classroom, when it comes to his own research, Lindemann turns to ITaP’s Snyder cluster, which is especially well-suited to life sciences research because of its high-memory nodes and fast access to research data storage.
Lindemann studies the gut microbiome and how diet affects the composition and function of the microbes in our digestive tracts. A high-memory supercomputer like Snyder is essential for performing next-generation sequence analysis and genome assembly to estimate the abundance and function of different microbes.
The availability of ITaP Research Computing resources and expert support played a major role in Lindemann’s decision to join the Purdue faculty last fall.
“If you don’t have a central supportive research computing system, you have to buy it at the individual lab level and that is much more expensive, and also requires that you maintain it and load all the required software,” says Lindemann. “So it’s been a huge plus to have ITaP Research Computing to help us get these things done.”