New supercomputer to aid genomics research

Feb 18, 2013

The National Center for Supercomputing Applications (NCSA) has gifted the Institute for Genomic Biology (IGB) a highly parallel shared memory supercomputer named Ember. Originally funded by the NSF, Ember will be managed by the High-Performance Biological Computing (HPCBio) group.

"We've been using Ember for a while now through the NCSA, mainly in computational genomics," said Victor Jongeneel, Director of HPCBio. "It can perform a lot of tasks that our existing systems just can't. Having it under our own management will allow us better access and faster results."

The Ember has become part of the IGB biocluster, adding 1536 cores and eight terabytes of memory spread across four nodes.

Ember was installed in the server room at the IGB after its October 1st decommission by the NCSA. It would cost two million to purchase today, and is only two years old. Ember will be available to anyone on campus for a service fee, which will be placed in a fund to replace the infrastructure as it becomes dated.

For ease of use, Ember runs a Linux operating system, and can be used in many applications including chemistry, fluid mechanics, and imaging. However, its most called for use at the IGB will likely be in genomics and transcriptomics research.

Currently, the Carver Biotechnology Center sequences DNA in short segments of around 250 base pairs. These thousands of segments, however, overlap and are distributed randomly, making it difficult to see the "big picture" of the genome. Ember's very large shared memory—2 terabytes in a single system—will enable the applications to run much more efficiently as they organize and connect these segments, and has already facilitated several projects.

"It will be a wonderful addition to our research community," said Jongeneel. "In the past, some projects like these were left incomplete, or spent thousands of dollars on computer time. This will enable larger projects that we've had trouble with in the past, and easier and transcriptome assemblies."

Explore further: New role for Twitter: Early warning system for bad drug interactions

Related Stories

Cray replaces IBM on U. of Illinois supercomputer

Nov 14, 2011

The University of Illinois says Seattle-based Cray Inc. will take over construction of the stalled $300 million Blue Waters supercomputer project, three months after IBM pulled out citing cost and technical concerns.

'Condor' brings genome assembly down to Earth

Jul 20, 2010

(PhysOrg.com) -- Borrowing computing power from idle sources will help geneticists sidestep the multimillion-dollar cost of reconstituting the flood of data produced by next-generation genome-sequencing machines.

Recommended for you

Cattle ID system shows its muzzle

14 hours ago

Maybe it sounds like a cow and bull story, but researchers in Egypt are developing a biometric identification system for cattle that could reduce food fraud and allow ranchers to control their stock more efficiently. The ...

Combining personalization and privacy for user data

19 hours ago

Computer scientists and legal experts from Trinity College Dublin and SFI's ADAPT centre are working to marry two of cyberspace's greatest desires, by simultaneously providing enhanced options for user personalisation alongside ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.