Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics

Franck Giacomoni (1) , Gildas Le Corguillé (2) , Misharl Monsoor (2) , Marion Landi (1) , Pierre Pericard (2) , Mélanie Pétéra (1) , Christophe Duperier (1) , Marie Tremblay-Franco (3) , Jean-Francois Martin (3) , Daniel Jacob (4) , Sophie Goulitquer (2) , Etienne A Thévenot (5, 6) , Christophe Caron (2)

1 UNH - Unité de Nutrition Humaine
2 SBR - Station biologique de Roscoff [Roscoff]
3 E20 - MetaToul AXIOM
4 Functional Genomic Center - Proteomic Facility [Bordeaux]
5 LADIS (CEA, LIST) - Laboratoire d'analyse des données et d'intelligence des systèmes (CEA, LIST)
6 MetaboHUB

The complex, rapidly-evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data preprocessing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets, and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment (VRE) built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange, and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB).

Keywords: ANNOTATION; IDENTIFICATION; MASS-SPECTROMETRY DATA; WEB SERVER; SOFTWARE

Domains: Bioinformatics [q-bio.QM]; Databases [cs.DB]; Genomics [q-bio.GN]; Quantitative Methods [q-bio.QM]

Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, et al.. Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics, 2015, 31 (9), pp.1493-1495. ⟨10.1093/bioinformatics/btu813⟩. ⟨hal-01123263⟩