The Institute for Systems Biology has enlisted the aid of the Arctic Region Supercomputing Center as it grapples with a growing number of computationally intense genomics and proteomics tasks.
Lee Hood, founder of the Seattle-based ISB, said the institute currently has no supercomputing capability. “What we’ve put together is a modest farm of Alpha and Sun machines and that’s it. We have intermediate computing capacity but it doesn’t really touch these kinds of problems.”
Now, through its joint partnership with the ARSC, located on the University of Alaska Fairbanks campus, ISB researchers will have access to cycle time on three high-performance supercomputers: a 272-processor Cray T3E, a 32-processor Cray SV1ex, and a 200-processor IBM SP. Combined, these systems provide theoretical peak performance of 570 gigaflops, according to ARSC spokeswoman Virginia Bedford. In addition, the ARSC offers over 300 tera- bytes of data storage capacity.
But the ISB won’t be the only one to benefit from the deal. The centers plan to establish cross-institute faculty appointments that will not only give ISB staff the computational power and know-how needed to tackle their enormous data sets, but will also broaden the scope of research conducted at the ARSC. While the center currently conducts research in climate and ocean modeling, space physics, and geology, Bedford said a better grasp of computational biology would allow ARSC and UAF researchers to pursue additional areas of interest, including the study of microbes in the Alaskan environments, medical genetics of Alaska natives, and the genetics of wildlife in Alaska.
“Once the researchers at UAF collect the base sequence data, they end up with a stream of genetic code. ISB houses some of the best researchers in the world to help the researchers at UAF make sense of this stream of information. This will allow the researchers … to begin developing their own computational models and facilitate such research in the field of Arctic life sciences,” Bedford said.
The 2,000-mile expanse between the two centers is spanned by the Pacific Northwest GigaPop network — an extremely high-bandwidth fiber optic connection that “makes it almost like having the supercomputing center in the next room,” Hood said. The link speed between Fairbanks and Seattle is OC-12, or 622 megabits per second, according to Bedford.
The GigaPop network made the choice of the ARSC over a supercomputing center somewhere closer to Seattle much easier, Hood said. In addition, the ISB’s George Lake — an astrophysicist who switched his focus to computational biology in joining the institute last year — has been involved in past collaborations with the center, “so he knew all the people up there and that made it very easy.”
A further selling point for the ARSC, according to Hood, was the fact that other supercomputer centers have relatively little cycle time on their machines. Additionally, Hood said, “They have people who are interested in helping us with the software — that is converting our algorithms into algorithms that are appropriate for the various kinds of supercomputers that they have.”
Hood said several ISB projects would see immediate benefits from the partnership. Ruedi Aebersold, for example, has developed a technique for quantitating different patterns of protein expression in cells of two different states. “Part of what this requires is searching for fragments of proteins through a database of the entire set of potential fragments that could be generated by all proteins and that takes a lot of cycles to do,” said Hood. “So the supercomputer center is an ideal place to go and have that kind of problem solved.”
The ISB research staff, which now numbers over 170, is also actively involved in comparative genomics — a computationally demanding task “even if you’re comparing microbes against microbes, let alone human genome against mouse genome,” Hood said.
“We have some really computationally intense problems both in genomics and proteomics and it looks like there’s the possibility of doing some really interesting things now,” he added.