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Rattlesnakes on a Jetstream

Speed read
  • Scientists use cloud-based HPC to perform genomic analysis of rattlesnakes 
  • Jetstream enables worldwide collaboration without extensive HPC training
  • On-demand, domain-specific virtual machines allow scientists to focus on their science 

Beneath a blazing sun in Arizona, a team of University of Arkansas researchers led by Marlis and Michael Douglas walk one-by one, single file. They swelter as they trek through hot and desolate canyons, yet their mission keeps their optimism high.

<strong>Marlis Douglas.</strong> The genetic diversity she encounters in her research is easily accommodated by the cloud based virtual machines Jetstream provides. Courtesy University of Arkansas.

Their task is not for the faint of heart. They’re out to collect blood samples from rattlesnakes for DNA analysis. The rattlesnakes have venom, and scientists risk death if bitten.

“One thing we always say is, you don’t find rattlesnakes, they find you,” says Marlis Douglas, professor in the department of biological sciences at the University of Arkansas.

The big data behind rattlesnakes  

But braving the rattlers is not the most challenging aspect of the research at the Douglas Lab.

Before the team can clarify if the rattlesnakes are different species and, in turn, promote venom research, they must first wade through an ocean of big data.

Fortunately, Jetstream can take these scientists to their destination.

The Douglas lab focuses on the quantification and conservation of biodiversity, a task that requires significant computational resources.

Jetstream, the National Science Foundation’s (NSF) first cloud-based resource for science, technology, engineering, and mathematics (STEM) disciplines, has easy-to-use high-performance computing (HPC) capabilities that promote scientific research by allowing large amounts of data to be processed.

“We obtain massive amounts of data by sequencing thousands of genes,” says Marlis Douglas. “These data are obtained from a single rattlesnake, but we actually need to sequence 500 snakes for a realistic estimate of their diversity. Those data simply cannot be analyzed by just using desktop computers.”

The virtue of virtual machines

Jetstream’s virtual machines (VM) allow scientists to easily collaborate, and to share computational research tools, which is a boon for the Douglas lab because they partner with scientists from different disciplines all over the world.

You don’t find rattlesnakes, they find you. ~Marlis Douglas

For example, the Douglas lab collaborates with scholars in Southeast Asia who work to conserve big river fishes, an approach that parallels similar efforts by the lab in the rivers of southwestern North America.

Another benefit that Jetstream offers scientists is the ability to effortlessly train researchers without a formal bioinformatics background to utilize HPC resources.

“Our team can set up a VM for collaborators at other institutions who haven’t been trained in a bioinformatics capacity, then teach them to apply a series of high-performance computing programs,” says Michael Douglas, also a professor in the department of biological sciences at the University of Arkansas.

<strong>Jetstream</strong> is the nation's first cloud based research computing resource. Courtesy Indiana University.

“Those collaborators can then analyze data and obtain results relatively effortlessly, and that’s very beneficial because it not only promotes their research capacity, but also educates them and many students in the STEM disciplines.”

Varieties of scientific experience

Jetstream is also useful for individual scientists because it allows them to customize computer programs for each project, because of the unique discrepancies that exist in biodiversity data.

“There is a considerable amount of variation in nature, and we work with many species from different areas — biodiversity data are noisy and unpredictable,” says Marlis Douglas.

“There are many unknowns and these require custom scripts and a flexible computing scheduling to analyze. Our local HPC resources have difficulties accommodating our specialized analyses and conditions.”

The genetic diversity among rattlesnakes creates difficulties in identifying distinct species, identification essential for the correct medical treatment of snakebites.

The HPC capabilities of Jetstream help researchers understand the geographic variation among rattlesnakes, ensuring that antidotes stocked at local hospitals are as specific as possible, and thus more effective.

<strong>Michael Douglas.</strong> Collaboration is the name of the scientific game today, says Michael Douglas. Jetstream brings the HPC tools that facilitate long distance scientific partnerships. Courtesy University of Arkansas.

Long distance relationships

The collaborative nature of today’s scientific research is also a departure from previous generations when scientific work was more individually focused.

However, Michael Douglas says that working with Jetstream provides the opportunity to reinforce with students the bigger picture of their research as they seek rattlesnakes in the blistering heat of Arizona.

“When I was a young professional, being collaborative was not considered a good strategy,” Michael Douglas says.

“It was all about what are you doing individually — show me what you’ve done. Now scientists collaborate extensively, as reflected in NSF- and National Institute of Health-funded studies. Students must now be trained not only to think collaboratively but also to employ a bigger picture, and that’s the sandbox provided for us by Jetstream.”

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