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Oxford University Press (OUP), Bioinformatics, 9(31), p. 1493-1495

DOI: 10.1093/bioinformatics/btu813

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Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Paper reference: Giacomoni et al. (2014) Workflow4Metabolomics: A collaborative research infrastructure for com-putational metabolomics. Bioinformatics http://dx.doi.org/10.1093/bioinformatics/btu813 ; In the context of an emergent and fast evolving science, the development of varioustools dedicated to metabolomic data processing and data analysis increased. Because metabolo-mic analyses require a variety of steps involving various disciplines from analytical chemistry tostatistics and bioinformatics, it requires many skills and expertise. However, despite this abun-dance of tools, standardization is lacking in these diversity of programs, as well as infrastructureto handle and link the different steps of metabolomic analyses. We recently implemented Work-flow4Metabolomics (W4M), a collaborative online platform hosting and providing a full pipelinefor metabolomics from data preprocessing to annotation including statistical analysis. It is notdesigned to respond to only one specific type of metabolomic analysis, but to cover a maximumrange of possible approaches - as metabolomics is a complex science that can be studied throughvarious complementary analytical techniques. Thus, more than just gathering programs, W4Mprovides relevant combinations of generic and specific tools, a large part of which being develo-ped and sustained by the partners providing this virtual research environment (VRE). Moreover,using Galaxy, a web-based platform technology, W4M provides modules from various sources andof various types. This platform allows hosted tools to be run and linked together via an instinc-tive and ergonomic interface, which is beneficial for both beginners and experts in metabolomics.W4M gets its strength from the collaboration of complementary teams from bioinformatics and me-tabolomics environment. Initiated by the collaboration between two platforms, it gathers today sixresearch teams and platforms with a higher diversity in skills and expertise. It allows a continuousenrichment in the service provided, with addition of new modules and new possible workflows de-dicated to cover a large scope of the increasing needs of the metabolomic community. Moreover,the ‘open-source’ aspect of this platform allows to open it to new collaborators bringing specificexpertise that can be highlighted and disseminated in the metabolomic community