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Southwest Foundation for Biomedical Research Doubles Compute Power with $1M AT&T Gift

The AT&T Foundation, based in San Antonio, Texas, has granted neighbor Southwest Foundation for Biomedical Research the ability to double its already-massive compute power.
The $1 million gift enabled SFBR to grow its “computer ranch” from 1,500 processors to 3,000. Specifically, the center has installed 375 new four-processor Opteron computers from vendor M&A Technologies of Carrollton, Texas.
Spokesperson April Borlinghaushaus told BioInform via e-mail that since 2,003 AT&T has provided the SFBR with more than $2.4 million in grant support that has “enhanced programs that help our scientific community get even closer to finding new methods of disease prevention and groundbreaking treatment possibilities.”
When asked to comment on future funding of SFBR, Borlinghaus said AT&T was not at liberty to disclose that.
John Blangero, AT&T Genomics Computing Center director, told BioInform that the gift follows a long history of philanthropy on the part of the telecommunications giant.
Tom Dyer, a staff scientist in the department of genetics, said SFBR began building its cluster more than a decade ago, starting out with “a few Pentium IIIs that have since been replaced.”
The legacy cluster was comprised of dual-processor Athlons with one GB of RAM, Dyer said. “These were purchased over time and thus vary in clock speed and so forth,” he explained via e-mail.
The new machines each contain two dual-core 1.8 GHz Opteron CPUs sharing 4 GB of RAM, he said.
“For testing purposes, we had previously bought another 24 of the same units, as well as 10 boxes each containing two single-core Opterons,” he wrote. That brings the total Opteron count to more than 1,600, he said, with the remainder of the cluster’s 3,000 CPUs being Athlons.
Blangero said the AT&T Foundation has been a long-time contributor to SFBR. He said that the AT&T Genomics Center was “largely built” with donations from the foundation in 2003. 
SFBR will use the upgraded cluster as part of its work to detect genes that influence susceptibility to heart disease, diabetes, brain disorders, and cancer.
The center has used a separate gift of $300,000 from the Elizabeth Huth Coates Charitable Foundation to buy an Illumina 1G Genetic Analyzer for sequencing.
Blangero said that sequencing is one focus for the center, but not its core mission. And he said he wouldn’t classify SFBR as “largely doing bioinformatics at all.” Rather, he said, “we are very much focused on statistical genetics.”

The upgraded computer “allows us to, hopefully, keep pace with this blossoming amount of data.”

The “real focus” of the center, he said, “is to relate sequence variation to phenotypic variation … We are very much into processing large bits of epidemiological data and relating sequence variation to disease. Our focus has been on localization of human disease-related genes.”
He said the center has developed some of the software used worldwide on such efforts, such as independent calculations for the identification of human genes.
“From the beginning we’ve developed [the software] so we could find all the independent calculations and be able to farm them out. Now we basically have a system that pretty much scales with the number of processors,” he said.
Dyer said that previously, the cluster didn’t have high-speed interconnect between the processors, which limited its computational capacity. “Imagine you have 100 people working on the same problem, not 100 versions of the same problem. … The first person can work a little while, the second person is working … then they have to stop and trade their results. It’s that time taken to trade results before they can move on” that was the problem before the upgraded system, he said.
Dyer said that SFBR’s genotyping capabilities have also expanded from being able to analyze only a few hundred samples to a million samples.
The upgraded computer, he said, “allows us to, hopefully, keep pace with this blossoming amount of data.”

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