Workflow4Metabolomics 3.0

Welcome to the collaborative portal dedicated to metabolomics data processing, analysis and annotation for Metabolomics community.

Follow us on Twitter  @workflow4metabo

W4M will migrate in 2020 on new server and computing infrastructure!

Our beta version is now available on:

Please ask for account here.

Data migration tutorial is available here.




Tools and workflows on W4M.

Archives : 2016 W4E course at CNRS, Roscoff, 2017 W4E course at Pasteur, Paris, 2018 W4E course at Pasteur, Paris and 2020 W4E course at ULB, Brussels.

In the context of collaboration between metabolomics (MetaboHUB French infrastructure) and bioinformatics platforms (IFB: Institut Français de Bioinformatique), we have developed full LC/MS, FIA-MS, GC/MS and NMR pipelines using Galaxy framework for data analysis including preprocessing, normalization, quality control, statistical analysis (Univariate, Multivariate PLS/OPLS) and annotation steps. Those modular and extensible workflows are composed with existing components (XCMS and CAMERA packages, etc.) but also a whole suite of complementary homemade tools. This implementation is accessible through a web interface, which guarantees the parameters completeness. The advanced features of Galaxy have made possible the integration of components from different sources and of different types. Thus, an extensible Virtual Research Environment (VRE) is offered to metabolomics communities (platforms, end users, etc.), and enables preconfigured workflows sharing for new users, but also experts in the field.

Publications :
Giacomoni F., Le Corguillé G., Monsoor M., Landi M., Pericard P., Pétéra M., Duperier C., Tremblay-Franco M., Martin J.-F., Jacob D., Goulitquer S., Thévenot E.A. and Caron C. (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics,

Guitton Y., Tremblay-Franco M., Le Corguillé G., Martin J.F., Pétéra M., Roger-Mele P., Delabrière A., Goulitquer S., Monsoor M., Duperier C., Canlet C., Servien R., Tardivel P., Caron C., Giacomoni F., Thévenot E.A., Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics, The International Journal of Biochemistry & Cell Biology, 2017, ISSN 1357-2725, This paper is also available on the open archive HAL.


We thank genotoul bioinformatics platform for computing/storage resources and webhmia team for web portal hosting.