Leveraging the national cyberinfrastructure for biomedical research

Members of several groups within the national cyberinfrastructure, each of whom has a role in supporting life science research, wrote a Perspective piece titled “Leveraging the national cyberinfrastructure for biomedical research,” that was published in the “Big Data” issue of the Journal of the Americana Medical Informatics Association. The paper can be downloaded at: http://jamia.bmj.com/content/early/2013/08/20/amiajnl-2013-002059.full. Authors represent Indiana University, the Texas Advanced Computing Center, Internet2, and the Pittsburgh Supercomputing Center.

Figure 1. A Roadmap to the Research Information Superhighway: over 200 supercomputer centers are interconnected across a series of high speed physical networks. The resources in these centers are shared across organizations such as XSEDE and OSG. Specialized centers use XSEDE and OSG to support specialized user communities.

Staff from five separate national cyberinfrastructure organizations worked together to invite medical informatics researchers to use existing systems that have been underutilized by medical researchers. If medical researchers increased their use of these and other cyber resources, they would be able to reduce their costs for high performance computing, as well as undertake larger analyses that are beyond their current compute resources. This article has been downloaded over 2,340 times in the last seven months.

This project represents five separately funded organizations working together to invite the medical informatics community to take advantage of existing national-scale resources to address “big data” challenges. Resources such as the Extreme Science and Discovery Environment, the Open Science Grid, and Internet2 provide economical and proven infrastructures for “big data” challenges, but these resources can be difficult to approach. Specialized web portals, support centers, and virtual organizations can be constructed on these resources to meet defined computational challenges, specifically for genomics. The paper provides examples of how this has been done in basic biology as an illustration for the biomedical informatics community.

NSF GSS Codes:
Primary Field: Genetics 610 - Genome Sciences/Genomics
Secondary Field: Computer Science 401 - Computer Systems Analysis

Project Lead: Rich LeDuc

National Center for Genome Analysis Support (NCGAS),UITS Research Technologies, research made possible by Mason

This research is based on work supported by the National Science Foundation under grant no. ABI-1062432 (Craig Stewart, PI) and 1242759 PHY to Indiana University.