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Paper ID: 1345

A GT3 based BLAST grid service for biomedical research
Micha,Bayer Aileen,Campbell Davy,Virdee

Appeared in: Proceedings of the UK e-Science All Hands Conference 2004 website: http://www.allhands.org.uk/2004/
Page Numbers:1019 - 1023
Publisher: Engineering and Physical Sciences Research Council
Year: 2004
ISBN/ISSN: 1-904425-21-6
Contributing Organisation(s):
Field of Science: e-Science

URL: http://www.allhands.org.uk/2004/proceedings/papers/141.pdf

Abstract: 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 an implementation of BLAST which is delivered using a grid service constructed with the Globus toolkit v.3. 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. To achieve maximum performance in a grid context, the service uses parallelism at two levels. Single query sequences can be parallelised by using mpiBLAST, a BLAST version that fragments the target database into multiple segments which the query sequence can be compared against in parallel. Multiple query sequences are 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 provided our own java based scheduler which distributes sub-jobs across an array of resources.

Keywords: e-Science, AHM 2004



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