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Combining a High-Throughput Bioinformatics Grid and Bioinformatics Web Services

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Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4360))

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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.

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Author information

Authors and Affiliations

  1. Sun Center of Excellence for Visual Genomics, University of Calgary, HS 1150, 3330 Hospital Dr. NW, Calgary, Alberta, T2N 4N1, Canada

    Chunyan Wang, Paul M. K. Gordon, Andrei L. Turinsky & Christoph W. Sensen

  2. National Research Council Institute for Marine Biosciences, 1411 Oxford Street, Halifax, Nova Scotia, B3H 3Z1, Canada

    Jason Burgess & Terry Dalton

Authors
  1. Chunyan Wang
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  2. Paul M. K. Gordon
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  3. Andrei L. Turinsky
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  4. Jason Burgess
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  5. Terry Dalton
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  6. Christoph W. Sensen
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Editor information

Werner Dubitzky Assaf Schuster Peter M. A. Sloot Michael Schroeder Mathilde Romberg

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© 2007 Springer Berlin Heidelberg

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Wang, C., Gordon, P.M.K., Turinsky, A.L., Burgess, J., Dalton, T., Sensen, C.W. (2007). Combining a High-Throughput Bioinformatics Grid and Bioinformatics Web Services. In: Dubitzky, W., Schuster, A., Sloot, P.M.A., Schroeder, M., Romberg, M. (eds) Distributed, High-Performance and Grid Computing in Computational Biology. GCCB 2007. Lecture Notes in Computer Science(), vol 4360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69968-2_1

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  • DOI: https://doi.org/10.1007/978-3-540-69968-2_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-69841-8

  • Online ISBN: 978-3-540-69968-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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