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Bioinformatics Advance Access originally published online on June 30, 2008
Bioinformatics 2008 24(16):1823-1825; doi:10.1093/bioinformatics/btn325
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

BioMAJ: a flexible framework for databanks synchronization and processing

Olivier Filangi 1, Yoann Beausse 2, Anthony Assi 1, Ludovic Legrand 3, Jean-Marc Larré 2, Véronique Martin 3, Olivier Collin 1, Christophe Caron 3, Hugues Leroy 1 and David Allouche 2,*

1IRISA/INRIA, Symbiose Project, 2Unité de Biométrie et Intelligence Artificielle, UR875, INRA, F-31320 Castanet-Tolosan and 3INRA Unité Mathématique Informatique et Génome, UR1077, INRA, F-78350 Jouy-en-Josas, France

*To whom correspondence should be addressed.


  Abstract

Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks.

Availability: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.

Contact: biomaj{at}genouest.org

Associate Editor: Dmitrij Frishman

Received on March 14, 2008; revised on June 20, 2008; accepted on June 20, 2008

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