A Team in Oregon is Tracking Endangered Owls by Sound Alone

When expertise corporations develop progressive new merchandise within the high-performance computing (HPC) house, it permits life science researchers to do new issues that they hadn’t imagined earlier than. And when life science researchers make new breakthroughs, it pushes data expertise to innovate new approaches to help these scientific advances. It’s a relationship that has pushed innovation within the life sciences business for years. 

This mutually helpful cycle is especially evident within the work of the Middle for Quantitative Life Sciences (CQLS) at Oregon State College. The middle helps greater than 26 totally different departments, offering laboratory gear, computing infrastructure, coaching, and entry to workers members with intensive expertise in genomics, bioinformatics, and computational biology.

Christopher Sullivan, the assistant director for biocomputing at CQLS, lately sat down for an interview the place he mentioned a number of the middle’s most enjoyable new initiatives. A number of of these initiatives use machine studying fashions to carry out superior analytics operating on the middle’s HPC clusters.

Monitoring Owls by Sound

Working with the U.S. Forest Service, researchers at Oregon State have developed algorithms that may determine totally different species of owls from sound alone. They arrange recording stations within the woods to seize audio information. They then generate spectrograms — visible representations of the audio inputs — which they analyze utilizing a machine studying mannequin they’ve skilled to acknowledge distinct species.

To start with, the fashions might solely determine a handful of species. However the crew saved their audio recordings through the years, about 5 PB captured because the Nineteen Nineties. Within the intervening years, the scientists developed extra fashions, in order that at present, the undertaking can determine greater than 50 totally different species. On the similar time, the expertise has superior, permitting the scientists to re-run that outdated knowledge extra rapidly than up to now.

“You give me a brand new expertise, I’m going to push as a lot knowledge out of that expertise as I presumably can,” Sullivan mentioned. “It’s about constructing the instruments that we’d like alongside the information because it comes at us. And as these instruments change, we’re in a position to return to the information and redo it.”

This scientific and technological breakthrough is having a significant affect on each the economic system and the atmosphere. “It’s serving to the general public monitor the owl populations and all the opposite animal populations within the forest in order that teams can farm the forests correctly for wooden and various things with out harming species,” Sullivan defined.

Monitoring Covid in Wastewater

Plenty of the work at CQLS includes genetic sequencing. For instance, they frequently analyze the genetic materials in wastewater in order that they’ll decide which Covid variants are most prevalent at any given time. 

That is an space the place a scientific breakthrough drove advances in computing. Sullivan defined {that a} new genome sequencing innovation enabled the CQLS to scale up in order that as an alternative of doing 2,000 sequences per run, they had been in a position to conduct 2 million sequences per run. And it occurred “actually in a single day.”

However the computing infrastructure wasn’t designed for that type of throughput. “So we truly had to return and develop a complete new stack as a result of the expertise modified,” Sullivan mentioned. “We’re continually doing that always.”

Figuring out Plankton by Laser Mild

One other CQLS undertaking is utilizing genetic sequencing to watch the well being of the ocean. Oregon State’s Hatfield Marine Science Middle is working with the Nationwide Oceanic and Atmospheric Administration (NOAA) on a undertaking that analyzes they plankton in seawater. They’ve a ship that drags a laser system behind it to seize pictures of the ocean. Because the lasers cross over the water, the plankton and different organisms within the water forged a shadow. The crew data video of these shadows, which they then analyze with HPC methods powered by GPUs to categorise the contents. 

That effort generates an amazing quantity of information — on the order of 100 TB per week. That was greater than the CQLS might affordably retailer and course of within the cloud. Nonetheless, the middle’s HPC atmosphere, constructed with Dell infrastructure that includes NVIDIA GPUs, supplied the fitting steadiness of efficiency and value.

Initiatives like these are serving to Oregon State be taught extra concerning the world through which we dwell and develop progressive new approaches to computing on the similar time. Their efforts are bettering life and well being whereas additionally pushing the boundaries of what’s potential with high-performance computing.

For extra data, learn the OSU buyer story right here. 

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