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Bioinformatics. 2008 Aug 15;24(16):1823-5. doi: 10.1093/bioinformatics/btn325. Epub 2008 Jun 30.

BioMAJ: a flexible framework for databanks synchronization and processing.

Author information

1
IRISA/INRIA, Symbiose Project, Unité de Biométrie et Intelligence Artificielle, UR875, INRA, F-31320 Castanet-Tolosan, France.

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.

PMID:
18593718
PMCID:
PMC3293366
DOI:
10.1093/bioinformatics/btn325
[Indexed for MEDLINE]
Free PMC Article

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