Distributed BLAST in a grid computing context

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    Author
    Bayer, Micha; SINNOTT, RICHARD
    Date
    2005
    Source Title
    Computational Life Sciences: Lecture Notes in Ccomputer Science
    Publisher
    Springer
    University of Melbourne Author/s
    Sinnott, Richard
    Metadata
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    Document Type
    Journal Article
    Citations
    Bayer, M., & Sinnott, R. (2005). Distributed BLAST in a grid computing context. Computational Life Sciences: Lecture Notes in Ccomputer Science, 3695, 241-252.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/28871
    Description

    Paper presented at the First International Symposium, Comp Life 2005, Konstanz, Germany, September 25-27, 2005.

     

    This is a post-print of an article whose final and definitive form has been published in Lecture Notes in Computer Science © 2005 Springer; the original publication is available at: http://www.springerlink.com

     
    Abstract
    The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems.
    Keywords
    Grid computing; BRIDGES project (Biomedical Research Informatics Delivered by Grid Enabled Services)

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