Combining a high-throughput bioinformatics grid and bioinformatics web services

Authors:
Chunyan Wang;Paul M. K. Gordon;Andrei L. Turinsky;Jason Burgess;Terry Dalton;Christoph W. Sensen
Affiliations:
Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, Alberta, Canada;Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, Alberta, Canada;Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, Alberta, Canada;National Research Council Institute for Marine Biosciences, Halifax, Nova Scotia, Canada;National Research Council Institute for Marine Biosciences, Halifax, Nova Scotia, Canada;Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, Alberta, Canada
Venue:
GCCB'06 Proceedings of the 2006 international conference on Distributed, high-performance and grid computing in computational biology
Year:
2007

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Abstract

We have created a high-throughput grid for biological sequence analysis, which is freely accessible via bioinformatics Web services. The system allows the execution of computationally intensive sequence alignment algorithms, such as Smith-Waterman or hidden Markov model searches, with speedups up to three orders of magnitude over single-CPU installations. Users around the world can now process highly sensitive sequence alignments with a turnaround time similar to that of BLAST tools. The grid combines high-throughput accelerators at two bioinformatics facilities in different geographical locations. The tools include TimeLogic DeCypher boards, a Paracel GeneMatcher2 accelerator, and Paracel BlastMachines. The Sun N1 Grid Engine software performs distributed resource management. Clients communicate with the grid through existing open BioMOBY Web services infrastructure. We also illustrate bioinformatics grid strategies for distributed load balancing, and report several nontrivial technical solutions that may serve as templates for adaptation by other bioinformatics groups.