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August 22, 2013

NCGAS Makes HPC a Mainstay Tool for Biologists

Ken Chiacchia

The National Center for Genome Analysis Support (NCGAS) at Indiana University has expanded its services to help biologists use high-performance computing, NCGAS’ manager announced at a July 23 presentation at the XSEDE13 conference in San Diego.

“Everybody has some computing skills,” said Richard LeDuc. “But when we get to these really high levels of skills” required for intensive bioinformatics, “they’re rarer and rarer.” NCGAS, he explained, exists to give biologists an entrée into the field at every level. 

NCGAS is funded by the National Science Foundation and is a collaboration across Indiana University, Pittsburgh Supercomputing Center (PSC), the San Diego Supercomputer Center (SDSC), and the Texas Advanced Computing Center (TACC). On the day of LeDuc’s presentation, NCGAS announced it was providing users with:

  • up to 50 TB of storage on IU’s Scientific Data Archive
  • services for long-term curation and publication of raw data and final results
  • letters of commitment for consulting, computation and data storage resources for users’ grant proposals

Other NCGAS resources LeDuc described included:

  • expert bioinformatics to support biologists with any level of technology literacy
  • an instance of the Galaxy research workflow tool developed at Penn State University with pre-installed data transfer, transformation, and analytical tools pre-installed
  • Rockhopper, a supercomputing cloud appliance hosted at IU
  • IU’s Mason large memory cluster, with 512 GB of RAM per node for assembly
  • the Data Capacitor, which offers 5 PB at 20 Gbps throughput
  • access to HPC resources such as PSC Blacklight and other SDSC and TACC supercomputers

LeDuc stressed that NCGAS offers users support at any level required. “Most projects … need very little help from us,” he said. “All they need are big computers and resources to run their analyses.”

Some researchers, though, need to enter bioinformatics at the ground level: “Other biologists don’t have anybody to provide HPC support,” he said, and NCGAS, thanks to its bioinformatics expertise, can fill the need. In one oceanography project, for example, NCGAS was able to provide genomic analysis and annotations for researchers who lacked the bioinformatic background to do this on their own.

The annual XSEDE conference, organized by the National Science Foundation’s Extreme Science and Engineering Discovery Environment (xsede.org) with the support of corporate and non-profit sponsors, brings together the extended community of individuals interested in advancing research cyberinfrastructure and integrated digital services for the benefit of science and society. XSEDE13 was held July 22-25 in San Diego; XSEDE14 will be held July 13-18 in Atlanta.

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