Building an OptIPlanet collaboratory to support microbial metagenomics

L. Smarr, P. Gilna, P. Papadopoulos, T. DeFanti, G. Hidley, J. Wooley, E. V. Armbrust, F. Rohwer, E. Frost, Future Generation Computer Systems, Volume 25, Issue 2, pp. 124-131. July 2008.

Abstract

We describe early experiments in the adoption of the OptIPuter architecture to provide data-intensive capabilities to several remote users of a large-scale, multi-year effort to organize and make publicly available data describing a wide variety of marine microbial ecologies, their genomic content, and the local environments in which they live—marine microbial metagenomics. Microbial genomes are millions of base pairs in length, requiring both a global view of the genome and the ability to zoom into detail interactively, enabled by the OptIPortal. We describe the design of a scientific data and compute server, enhanced by OptIPuter technologies, and early examples of its use in support of high-performance science applications in this emerging scientific field.

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