Distributed, On-Demand, Data-Intensive and Collaborative Simulation Analysis

This project focuses on grid-enabling tools that can be used by a variety of content areas. At iGrid, these concepts are applied to a bioinformatics research area, specifically predicting identifiable intron/exon splice sites in human genes based on RNA secondary structures.

The modeling and simulation program, RNAfold, previously limited to under 30K base pairs, has been modified to scale with the available computing resources. The thermodynamic calculations now use grid services, and run in parallel at geographically distributed supercomputer centers, allowing a tractable solution to very large DNA sequences, typically over 100K in the human genome. The results are visualized in a collaborative environment, displaying spatial relationships and new insights into the identification of exonic splicing enhancers.

Contact
Arthurine Breckenridge
Sandia National Laboratories (SNL), USA
arbreck@sandia.gov

Collaborators
Arthurine Breckenridge, Geoff McGirt, SNL, USA
Sergiu Sanielevici, Pittsburgh Supercomputing Center, USA
Satoshi Sekiguchi, Tsukuba Advanced Computing Center, Japan
Fang-Pang Lin, National Center for High-Performance Computing, Taiwan
Matthias Mueller, Uwe Wössner, High Performance Computing Center Rechenzentrum Universität Stuttgart, Germany
John Brooke, Manchester Computing Centre, UK

http://www.cs.sandia.gov/ilab
http://www.tbi.univie.ac.at/research/VirusPrj.html
http://www.hlrs.de