SCIENCE

U.S. researchers are in the midst of dramatic developments in genome sequencing capabilities, driven by the availability of high throughput, low cost next-generation gene sequencers. To help address the scientific challenges of understanding this new wealth of gene sequence information, the National Science Foundation (NSF) has awarded Indiana University a $1.5-million grant to establish the National Center for Genome Analysis Support (NCGAS).

NCGAS will support the national community of NSF-funded researchers who undertake genome science, which is critical to new opportunities in biological discovery.

"This center will give biologists the tools to analyze gene sequence data that they cannot now study using existing systems," said William Barnett, director, Science Community Tools at IU. "We plan to enable innovative and potentially transformative genomics research by providing tools and services that will accelerate important new scientific discoveries."

Barnett is co-principal investigator and will direct the new center.

Current gene sequencers make it possible to obtain the sequence of DNA fragments in a human genome much faster than when the human genome was first published in 2001. However, these new sequencers produce the genetic information in many, much smaller pieces, and assembling this information into a full genome—so its overall function can be understood—is dramatically more difficult than with earlier sequences.

NCGAS will support the use of genome analysis software, store the data sets, and be a repository of open source genome analysis software.

The center will also provide dedicated access to large memory supercomputers such as IU's new Mason system. Each Mason compute node has 500GB of random access memory, critical for data-intensive science applications such as genome assembly. Mason's integration with the new NSF-funded Extreme Science and Engineering Discovery Environment (XSEDE) will provide campus-based integration known as "campus bridging." Indiana University is a funded partner in XSEDE.

IU's partners in NCGAS include the Texas Advanced Computing Center (TACC) at the University of Texas Austin and the San Diego Supercomputer Center (SDSC) at the University of California San Diego. NCGAS will support genome analysis software running on supercomputers at TACC and SDSC, as well as other supercomputers that are part of XSEDE. The collection of supercomputers included in XSEDE makes it one of the most advanced, powerful, and robust collections of integrated advanced digital resources and services in the world.

The center leverages the expertise and intellectual leadership of Co-Principal Investigators Michael Lynch, distinguished professor of biology; Matthew Hahn, associate professor of biology and informatics; and Geoffrey C. Fox, director of the Pervasive Technology Institute's Digital Science Center and distinguished professor of informatics. The NCGAS grant award will fund three new positions at IU.

Craig Stewart, dean for Research Technologies, executive director of PTI, and principal investigator on the NCGAS grant award, said, "The NCGAS is the culmination of more than a decade of focused support for bioinformatics by University Information Technology Services, spearheaded initially by Dr. Richard Repasky and now led by Dr. William Barnett. Dr. Repasky was in failing health as he helped write this proposal—which turned out to be the last in which he was involved. Dick passed away last fall after a long battle with cancer, and we are grateful to have NCGAS as one element of his legacy at IU. Here's to you, Dick Repasky!"