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High Performance Blast over the Grid

Abstract : As grids become more and more attractive for solving complex problems with high computational and storage requirements, bioinformatics algorithms start to be ported on large scale platforms. The BLAST kernel was one the first application ported on such platform. However, although simple parallelization was enough for the first proof of concept, its use in production platform needed more optimized algorithms. The chapter reviews existing parallelization and “gridification” of the BLAST algorithm as well as related issues such as data management and replication. A case study using the DIET middleware over the Grid'5000 experimental platform is also presented.
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Submitted on : Monday, March 2, 2009 - 4:11:16 PM
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Vincent Breton, Eddy Caron, Frédéric Desprez, Gaël Le Mahec. High Performance Blast over the Grid. Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare, Medical Information Science Reference, 121-148 p., 2009, ⟨10.4018/978-1-60566-374-6.ch007⟩. ⟨in2p3-00365202⟩



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