Indiana University's Genomics Grid wins High Performance Computing Challenge at SC2003

Bloomington 04 December 2003A team led by University Information Technology Services (UITS), the Indiana University Center for Genomics and Bioinformatics (CGB), and the High Performance Computing Center of the University of Stuttgart (HLRS) won a prestigious High Performance Computing Challenge award last November at SC2003, a major annual international supercomputing conference. Their project, "Global analysis of arthropod evolution", took top honours in the category of "Most Geographically Distributed Application". The HPC Challenge, held each year at the conference, brings together the world's leading experts in supercomputing to demonstrate new capabilities in supercomputing and Grid computing.

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The winning project addressed the long-held belief that arthropods with six legs, insects and their relatives, constitute a single evolutionary family. This has become a topic of hot debate among biologists in the past two years, and settling the matter has been difficult because of the tremendous amounts of computing time required to analyse these evolutionary relationships. "The data we needed were available as a result of genome sequencing projects", stated John Colbourne of the Center for Genomics and Bioinformatics. "The critical problem was getting the computing resources in place."

To create the computing resource required for this demonstration, UITS and HLRS, with the help of many partners worldwide, assembled a global Grid spanning every continent but Antarctica. The software used in this project included fastDNAml, a parallel programme for studying evolutionary relationships, maintained by Indiana University (IU), along with Grid middleware and collaborative tools created by HLRS. fastDNAml is one of few biological programmes that will run effectively on hundreds of processors in a computing Grid, and has practical applications in the study of infectious diseases as well as its applications in theoretical studies of evolution.

Also as part of this project, UITS demonstrated new enhancements to visualization software developed by the Advanced Visualization Laboratory (AVL). This follows the recent announcement about commercialization of new hardware developed by the AVL and demonstrates the breadth of the lab's involvement from basic scientific research to economic development through technology transfer.

TeraGrid resources played an important role in the Grid assembled to solve this challenge problem. Key components of the IU contribution to the Grid included the NSF-funded AVIDD system and computing facilities of the Lilly Endowment- supported Indiana Genomics Initiative. HLRS, the European e-Science effort, and Asian Grid facilities provided other significant facilities. The TeraGrid is the United States' flagship effort to create a national cyberinfrastructure, or massive network of giant supercomputers, massive storage systems, and advanced instruments that will make possible breakthrough research in many scientific disciplines. Indiana University and Purdue University were recently awarded a grant to join in the building of the TeraGrid.

And are six-legged arthropods one evolutionary family or not? "It's too early to tell", explained John Colbourne. The analysis continues, with submission of a scientific paper expected within a few weeks.


Leslie Versweyveld

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