Pico Computing Demonstrates Bioinformatics Acceleration at SC 2011

Pico's SC5 FPGA cluster reduces short read sequencing from 6 1/2 hours to just one minute

Seattle, WA (PRWEB) November 09, 2011

Pico Computing will be demonstrating an FPGA implementation of BFAST resulting in a 350X acceleration over a software-only implementation running on two quad core Intel Xeon processors. The 350X acceleration was achieved using 8 Pico M-503 FPGA modules in their SC5 SuperCluster chassis. The BFAST algorithm is primarily used in short read genome mapping.

Read more: http://www.sfgate.com/cgi-bin/article.cgi?f=/g/a/2011/11/09/prweb8945226.DTL#ixzz1dyI5LQs

NSF Gives Three Life-Science Projects $1.2M Grant to Test Microsoft’s Azure Cloud

Three life-science projects are among 13 teams that will have free access to Microsoft’s Azure cloud-computing platform for two years as part of an agreement between Microsoft and the National Science Foundation.

The life-science projects, led by researchers at Virginia Polytechnic Institute; the University of North Carolina, Charlotte; and the J. Craig Venter Institute, were awarded a total of $1.2 million in grants under the program, which kicked off in 2010 (BI02/10/2010). The awardees were announced last week.

In addition to providing access to the cloud, Microsoft will provide a support team, tools, applications, and data collections to help the scientists integrate cloud technology into their research.

An NSF review board considered the “appropriateness” of each proposal to the Azure platform’s capabilities, Reed Beaman, a program director at the agency, told BioInform.

For example, he said, the reviewers considered the fact that the platform is very strong in so-called “embarrassingly parallel” computations and in its ability to deploy web services.

He observed that in addition to providing Microsoft an opportunity to test the limits of its cloud computing platform, the partnership saves research dollars that would otherwise have been spent on hardware.

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U of Minnesota Spends $3.6M NIH Grant on Supercomputer for Biological and Medical Research

The University of Minnesota Supercomputing Institute for Advanced Computational Research has installed a new high-performance computing system from SGI, christened Koronis, that it will use for multi-scale modeling, chemical dynamics, bioinformatics, computational biology, and biomedical imaging.

The university purchased the 1,152-core system with a $3.6 million grant from the National Institutes of Health's National Center for Research Resources. It will support NIH-funded research projects at the university.

Jeff McDonald, assistant director of high-performance computing operations at MSI, told BioInform that the latest purchase is the largest system at MSI and that it was selected because its shared memory capabilities best fit the researchers' needs.

In the grant abstract, the researchers wrote that the new system will help 33 research groups supported by 91 NIH grants "tackle ... the acquisition, analysis and visualization of petascale data from high-performance computing and high-throughput technologies."

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