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. 2014 Mar-Apr;21(2):195-9.
doi: 10.1136/amiajnl-2013-002059. Epub 2013 Aug 20.

Leveraging the national cyberinfrastructure for biomedical research

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Leveraging the national cyberinfrastructure for biomedical research

Richard LeDuc et al. J Am Med Inform Assoc. 2014 Mar-Apr.

Abstract

In the USA, the national cyberinfrastructure refers to a system of research supercomputer and other IT facilities and the high speed networks that connect them. These resources have been heavily leveraged by scientists in disciplines such as high energy physics, astronomy, and climatology, but until recently they have been little used by biomedical researchers. We suggest that many of the 'Big Data' challenges facing the medical informatics community can be efficiently handled using national-scale cyberinfrastructure. 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. We provide examples of how this has been done in basic biology as an illustration for the biomedical informatics community.

Keywords: Big Data; Genomics; National Cyberinfrastructure.

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Figures

Figure 1
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.
Figure 2
Figure 2
Users and number of compute jobs submitted through the Galaxy Main web-portal by month.
Figure 3
Figure 3
Schematic representation of current international data network connectivity available for scientific research.

References

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