Researchers and Research Computing Resources at URI: A Powerful Symbiosis

While URI researchers need not require exceptional computational power to benefit from its research computing resources, sometimes it is downright essential to have a bit more oomph. That is the case for Dr. Roxanne Beinart, an Associate Professor of Oceanography at the Graduate School of Oceanography.

Dr. Beinart’s research examines symbiotic relationships between microbes and other organisms in the ocean. Symbiotic relationships with ocean microbes are incredibly common and influence anything from global primary productivity, to biogeochemical cycling, to oceanic food webs, making it an important topic to understand. As it turns out, microbial ecologists like Dr. Beinart also commonly enter into symbiotic relationships with high-performance computing centers, which can be essential for conducting the gene and genomic sequence work central to their research. “There’s a step that we do in many of our analyses where you have all of these little bits of genetic data, like short sequences, and you’re trying to put them all together and assemble them into one longer sequence,” Dr. Beinart explained. “We needed access to high-memory nodes because these assembly processes require a lot of memory.”

These methods were instrumental in Dr. Beinart’s recent work investigating the impact of a 2022 volcanic eruption on animal and bacterial symbiont populations in Pacific deep-sea hot springs. Ash from the eruption covered a lot of these communities and killed a lot of organisms, but as Dr. Beinart’s work showed, genetic diversity was only lost in the bacterial partners rather than in the animal populations. The reason for this, per Dr. Beinart, was that “Animals don’t actually vary that much by site; they’re sort of genetically homogeneous across all of the sites, whereas the bacteria are really different at each site. When you decimate [a site] that pool of [bacterial] strains is lost.”

Dr. Beinart’s lab makes ample use of Unity, a high-performance computing cluster housed at the Massachusetts Green High-Performance Computing Center in Holyoke, MA. URI is a partnering institution at the Unity cluster, which means that Unity is free to use for URI researchers like Dr. Beinart. This removes a common logistical hurdle for studies that require substantial computing resources and can allow researchers’ grant dollars to go further. “When I started at URI they had just kind of started their high-performance computing cluster effort”, recalled Dr. Beinart. “For many years, until Unity, I used other resources through EPSCoR. It has been wonderful to see over the last few years Gaurav [Khanna, AVP of Research Computing at URI] taking the lead and the new research computing groups… We’ve had this real acceleration of research computing at URI.”

Dr. Beinart is excited about the potential for future computational research in genomics and bioinformatics that leverages public data. “The amount of genetic information that’s available is rapidly expanding,” she remarked. “Anna [Schrecengost, a PhD. candidate in the Beinart lab,] had a big project where she did a global meta-analysis of genomic datasets using thousands of datasets from thousands of samples from all over the global ocean… Figuring out ways to use those and leverage those I think is important and something I’m really interested in.”

As the amount of available data balloons, it begs the question of whether machine learning can be applied to bioinformatics and genomics. Sure enough, according to Dr. Beinart, machine learning is indeed being applied at the cutting edge of her field. While her lab may dive more into these techniques in the future, it already benefits from machine learning in the form of generative AI. “My own students are relying on ChatGPT or other AI to help them with their coding,” noted Dr. Beinart. “I’m interested to see if that makes things more accessible to a larger number of students. [Coding] can be a barrier to many students, or even to their interest in the kind of work we do.”

Finally, in good keeping with her instincts to encourage broader participation in science, Dr. Beinart urged other URI researchers considering leveraging URI’s research computing resources to jump right in. She has found content provided by the URI Institute for AI and Computational Research, like its AI Lab workshops, helpful, but her lab has learned even more from playing around in the system. In Dr. Beinart’s words, “A lot of this stuff just has to be something you try… You just have to get your hands in there and start doing things!”

So, take it from the pros, folks – if you think your work could benefit from URI’s research computing resources, your best option is just to give it a try. It could be the start of the another fruitful symbiosis!

Thanks to Dr. Roxanne Beinart for taking the time out of her schedule, during her sabbatical no less, to be interviewed for this piece. You can read more about her research here: https://www.mghpcc.org/project/sailing-the-symbiosis-seascape/

Written by Joshua Port
Ph.D. student at GSO