The University of Idaho Argonaut

The floor is raised about a foot off the ground. Four huge air conditioners cool down a hot room full of black towers. Meanwhile, a block of stacked beige monitors flicker with an occasional image before retuning to black.
This is the University of Idaho Bioinformatics Core Facility, a cluster of supercomputers used in scientific data analysis.
“Jorge’s working,” said Trent Nelson, system administrator.

Jorge is a graduate student from Montana who uses the cluster via webcam for his computer science research. He is analyzing the way an image is presented on-screen as part of his doctoral dissertation.
The Initiative for Bioinformatics and Evolutionary Biology has generated over $30 million in grant money, some of it funding the cluster. It began with 64 desktop computers, and has expanded into what will be its fourth generation, with more than 500 supercomputing processors in the cluster.

Researchers in biology and other departments use the center for data processing and number crunching. Biological sciences professor Jack Sullivan said it is a great recruitment tool for grad students and it helps bring a lot of young scientists to UI.
The facility has gone from simple beginnings as a “Beowulf cluster” in the Janssen Engineering Building, where several motherboards melted during the summer due to overheating, to its present home in McClure Hall.

“We have built research facilities that rival any in the country,” said Rob Lyon, system administrator.
Lyon said faculty from schools like Stanford and Harvard have visited this supercomputing center and been amazed.
Assistant professor Luke Harmon said he uses the supercomputing facility for statistical analysis in his research, which is also funded by money from IBEST. Harmon studies biofilms, structures that occur when bacteria produces a moist “goo” to adhere to a surface. One common example of a naturally occurring biofilm is the plaque found on teeth.

Biofilms are resistant to all antibiotics, and the only way to get rid of a biofilm infection is to remove the surface it is attached to. Cystic fibrosis patients are unable to control the infections in their lungs, which is why the disease is fatal.
“At first, I didn’t care whether it had practical implications,” Harmon said.

His earlier work studied differentiation in lizard populations. Now, he said he is taking the experience he’s gained with them and transferring it to the biomedical field. The common notion had been biofilms were resistant to antibiotics because of their structure, Harmon said, but his research is taking a different angle. He looks at the possibility the differentiation between the genetic make-ups of the bacteria in the biofilm is what causes them to be so hardy, taking an evolutionary perspective on this biological problem.

Sullivan said he also uses the facility to study evolutionary trees by finding statistical methods that make it easier to determine how species are related, as well as data analysis for his work with cedar hemlock forest ecosystems in the Pacific Northwest.
IBEST allows individuals outside of its organization to use the facility for a nominal operating fee, allowing researchers from the College of Natural Resources and the physics and math departments to use the cluster for data analysis.

“We have a crazy mix of people who would never get together,” Harmon said. “We get hardcore mathematicians that understand the language of biology.”
Sullivan said he wants the cluster to become a regional center for rural western states, which will require additional grant money. He said he hopes it will encourage interdisciplinary collaboration.

“An insane amount of computer analysis goes into what we do,” he said. “People like to work together … not just focus on areas that they know, and collaborate with others that have different scientific backgrounds.”