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SGI Powers Bioinformatics Research at U South Carolina


The University of South Carolina has upgraded its server and storage technologies to support research in bioinformatics and processing of medical images. The university adopted server and storage solutions for SGI, including the company's SGI Altix 4700 system and InfiniteStorage 4000.

The purchase was made using a grant from the National Science Foundation through James River Technical, an SGI higher education reseller. It includes 10 TB of storage, which, acording to U South Carolina, is "by far" the largest shared memory system in South Carolina in use at an academic institution. The system, installed back in April, is being used initially for five research projects: microbial genome research, an exploration of "phylogenetic reconstruction and multiple sequence alignment," a study of protein backbone structure data, a solution for medical image processing visualization problems, and "issecting gene regulatory networks to develop large-scale microarray data analysis incorporating comparative genomics information."

"For the data intensive needs of this research we needed a shared memory system, and there aren't many out there that are true shared memory--that was the primary reason we selected SGI Altix," said Duncan Buell, chair of the U South Carolina Department of Computer Science and Engineering, in a statement released this week. "The Altix met our specifications while delivering superior price-performance. In addition to the bioinformatics research, another reason we needed a shared memory machine is for medical image processing. If you're going to track a part of an image that you have identified, from one frame to the next--because people move from one frame to the next and the heartbeat causes registration problems in either video or MRIs--then you need to hold the frames in memory simultaneously. And you need to have space to store high-resolution images, which is why we bought as much storage as we could."

U South Carolina researchers will aso be developing code for the system to test new algorithms related to open-source phylogenetics program GRAPPA, originally developed out of the University of New Mexico and the University of Texas at Austin. U South Carolina said it intends to share the SGI system with other institutions in the state.

"The new system will significantly increase the available computational power that our computer clusters provide biomedical researchers in South Carolina," said Jijun Tang, assistant professor in the Department of Computer Science and Engineering. "We are creating a high performance computing center to increase the availability of these computational resources to researchers in the state of South Carolina."

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About the author:David Nagel is the executive editor for 1105 Media's online education technology publications, including THE Journal and Campus Technology. He can be reached at [email protected].

Proposals for articles and tips for news stories, as well as questions and comments about this publication, should be submitted to David Nagel, executive editor, at [email protected].

About the Author

David Nagel is the former editorial director of 1105 Media's Education Group and editor-in-chief of THE Journal, STEAM Universe, and Spaces4Learning. A 30-year publishing veteran, Nagel has led or contributed to dozens of technology, art, marketing, media, and business publications.

He can be reached at [email protected]. You can also connect with him on LinkedIn at .

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