They may not be powered by a major supercomputing center or a national lab, but at Bowdoin College – a private liberal arts college in southern Maine – biology students are putting HPC to good use. Using Bowdoin’s in-house HPC cluster, the team is delving into the genome of a noisy mainstay of American life: the common field cricket.
Specifically, the students’ objective is to generate the most complete transcriptome – the range of messenger RNAs (mRNAs) in a given tissue – of the field cricket to date: and moreover, to do it within just a few months. The cricket was chosen for its startling ability to “reorganize” its auditory system if one of its ears has been incapacitated, which the researchers hope might be partially explained through mRNA analysis.
Bowdoin’s in-house cluster, which has been continuously upgraded since its initial installation in 2008, currently stands at 1,192 CPU cores and 9 GPU nodes. The racks are housed at the FirstLight datacenter, which connects to Bowdoin via a fiber line.
Bowdoin is an undergraduate-only college, so the students involved in the project are all relatively new to high-performance computational biology. The professor organizing the project – Hadley Horch, a professor of biology and neuroscience at Bowdoin – worked with the nearby Mount Desert Island Biological Laboratory (MDIBL) to have a few of their bioinformaticians join the students weekly via Zoom. When the time comes to prepare and run the jobs, they are assisted by Dj Merrill, director of high-performance computing at Bowdoin.
“This is the first time we’ve seen the three [Bowdoin, MDIBL and Bowdoin’s HPC] coming together to actively teach a class,” Merrill said in an interview with Bowdoin’s Rebecca Goldfine.
Once the initial work is completed – which they plan on taking around three weeks – the students will work on annotating and curating the transcriptome, as well as using wet-lab work to identify gene expression before and after the field crickets’ auditory rewiring process.
“They’ll pick one gene to focus on, dissect tissue and do measurements on that gene to see if it is up- or down-regulated as we predicted,” Horch said. “These two strands will come together nicely – the bioinformatics and the wet lab research—so students can see how you build this resource and how you play with it experimentally as well.”
“It is ambitious what we’re trying to do,” Horch added. “And we have more plans, too, after we build this.”
For the students, this kind of hands-on HPC experience in their undergraduate careers represents important skill development.
“I spoke to a few neuroscience PhD candidates and researchers recently, and one of the questions I asked was ‘what is a skill that you didn’t get in college do you wish you had?’” said Lucy O’Sullivan, a student at Bowdoin. “And a lot of them said gaining proficiency in computer coding, especially as technology advances, that you have to keep up with the technology.”
Read Rebecca Goldfine’s reporting here.