Integrating GALAXY workflows in a metadata management environment

Francois Moreews 1, 2 Yvan Le Bras 3 Olivier Dameron 4 Cyril Monjeaud 3 Olivier Collin 3
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE, Inria Rennes – Bretagne Atlantique
3 Plateforme bioinformatique GenOuest [Rennes]
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique
4 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : The Galaxy platform offers repositories of user data and related analysis processes (data histories and workflows). These repertories enable traceability and reproducibility of the processes within the platform. At a larger scale, to answer questions like "What protocol was used to analyze my data?" or "how were these data generated?", we could consider any protocol as a metadata set that annotates inputs and results.We present a preliminary approach for integrating the GALAXY workflows in an extensible meta-data management environment.Using ISA-tools, we have developed a formalism to describe an abstraction of data processing workflows. This specification, in the ISA-TAB format is named ISA-DATAFLOW.A conversion tool extracts a structured dataflow representation in GRAPHML, a generic XML graph format, from GALAXY workflows. This intermediary format can then be normalized using controlled vocabularies and converted into ISA-TAB following our ISA-DATAFLOW specification.We plan to integrate this work to propose advanced research functionalities within a virtual research environment (VRE) deployed on a geographically and thematically distributed infrastructure already using multiple Galaxy instances. Future developments will concern workflow meta-analysis and workflow composition assistance.
Type de document :
Communication dans un congrès
Galaxy Community Conference, Jul 2014, Baltimore, United States. 2014
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https://hal.inria.fr/hal-01093058
Contributeur : Francois Moreews <>
Soumis le : mercredi 10 décembre 2014 - 09:45:05
Dernière modification le : mercredi 2 août 2017 - 10:09:24

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  • HAL Id : hal-01093058, version 1

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Francois Moreews, Yvan Le Bras, Olivier Dameron, Cyril Monjeaud, Olivier Collin. Integrating GALAXY workflows in a metadata management environment. Galaxy Community Conference, Jul 2014, Baltimore, United States. 2014. 〈hal-01093058〉

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