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Other Publications Year : 2007

BioMAJ : A workflow engine dedicated to biological bank management

Abstract

BioMAJ (BIOlogie Mises A Jour) is a workflow engine dedicated to biological bank management. The Software automates the update cycle and the supervision of the locally mirrored bank repository. This project is a collaborative effort between two French Research Institutes INRIA (Institut National de Recherche en Informatique et en Automatique) & INRA (Institut National de la Recherche Agronomique). Biological knowledge in a genomic or post-genomic context is mainly based on transitive bioinformatics analysis consisting in an iterative and periodic comparison of data newly produced against corpus of known information. In lab context, this approach needs accurate bioinformatics software, pipelines, interfaces and numerous heterogeneous biological banks, which are distributed around the world. An integration process that consist in mirroring and indexing those data is obviously an essential preliminary step which represents a major challenge and bottleneck in most bioinformatics projects; BioMAJ aims to resolve this problem, by proposing a flexible fully automated environment among the French genopole network, and/or any other network. Major Features: - Multiple Remote protocol ( ftp, http, rsync , local copy); - Powerful Exception Handling; - Data transfers integrity check; - Advanced workflow description (D.A.G) using Easy normalized syntax language; Post-process indexation for various bioinformatics software (blast, srs, fastacmd, readseq, etc ...); Easy integration of personal scripts for bank post-processing automation; History Graph generation for better bank repository analysis; Reporting facility: automatic Web report generation; Alert facility for the update cycle supervision.
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Dates and versions

inria-00176506 , version 1 (03-10-2007)

Identifiers

  • HAL Id : inria-00176506 , version 1

Cite

David Allouche, Anthony Assi, Yoann Beausse, Christophe Caron, Olivier Filangi, et al.. BioMAJ : A workflow engine dedicated to biological bank management. 2007. ⟨inria-00176506⟩
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