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High Performance Blast over the Grid
Breton V., Caron E., Desprez F., Le Mahec G.
Dans Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare (2009) 121-148 p. - http://hal.in2p3.fr/in2p3-00365202
Informatique/Bio-informatique
Sciences du Vivant/Bio-Informatique, Biologie Systémique
Informatique/Calcul parallèle, distribué et partagé
High Performance Blast over the Grid
V. Breton1, Eddy Caron (, http://graal.ens-lyon.fr/~ecaron)2, Frédéric Desprez ()2, Gaël Le Mahec1
1 :  LPC - Laboratoire de Physique Corpusculaire [Clermont-Ferrand]
http://clrwww.in2p3.fr/
CNRS : UMR6533 – IN2P3 – Université Blaise Pascal - Clermont-Ferrand II
Campus des Cézeaux 24, avenue des Landais BP 80026 63171 Aubière Cedex
France
2 :  INRIA Grenoble Rhône-Alpes / LIP Laboratoire de l'Informatique du Parallélisme - GRAAL
http://graal.ens-lyon.fr/
CNRS : UMR5668 – INRIA – École Normale Supérieure (ENS) - Lyon – Université Claude Bernard - Lyon I (UCBL) – Laboratoire d'informatique du Parallélisme
LIP, ENS Lyon, 46 allée d'Italie, 69364 LYON cedex 07 France
France
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.

Chapitres d'ouvrages scientifiques
2009
Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare
121-148 p.
Medical Information Science Reference

volumes 1 et 2, chapitre VII