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Board Connection Nets RIT a Bioinformatics Beowulf via IBM s SUR Award Program


It helps to have friends in high places. Bioinformatics researchers at the Rochester Institute of Technology now have access to a 104-processor IBM Linux cluster, largely due to the efforts of Susan Puglia, vice president of E-Server design at IBM, who also sits on RIT’s board of trustees.

The university received an equipment grant under IBM’s Shared University Research (SUR) program, an initiative to support academic research projects in areas of mutual interest, including life sciences, grid computing, and deep computing. According to IBM, it awarded nearly 30 SUR awards for bioinformatics research to universities and research institutes in 2002.

Investigators can’t apply for the SUR awards, however; they must be nominated by an IBM employee. That’s where Puglia’s connection to RIT comes in. As a member of the board of trustees, she initiated the grant process at IBM to secure a spanking new 104-processor Linux cluster with 4 terabytes of online storage for the university’s bioinformatics group.

The cluster is still being installed, but Gary Skuse, director of bioinformatics in RIT’s Department of Biological Sciences, already has a full workload scheduled for the system. The bioinformatics group had access to some dedicated computational resources before the equipment grant, “but not of this caliber,” Skuse noted. The new number-crunching power will support bioinformatics projects at RIT in the areas of comparative genomics and text mining, as well as the development of a database on protein sub-domains that the university hopes to make publicly available. For many of these projects, “the software is ready to install the day I say it’s okay,” Skuse said.

Along with the equipment grant, SUR recipients engage in research collaborations with IBM researchers working in similar areas. Skuse said that IBM and RIT have just begun exploring possible collaborative projects and have “identified what looked to be some fruitful opportunities.” One likely area of cooperation is in the identification of genes involved with late-onset hearing loss, as researchers at both RIT and IBM are working in this area.

Skuse noted that IBM donated the servers, but RIT funded the rest of the cluster architecture. Approximately 20 researchers in the bioinformatics group will have immediate access to the system, but Skuse said it would be shared with anyone else at RIT who wants to use it as well.

— BT

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