What is Galaxy W4M ?

Our project

The , in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform. It was created in 2012 by Metabomer and Abims labs in order to provide an integrated analysis environment for Metabolomics. Since, other contributors joins us and now we are actually an international team of dozen of peoples from several Labs.

In a collaborative efforts between metabolomics ( French infrastructure ) and bioinformatics platforms ( Institut Français de Bioinformatique ), we’ve crafted comprehensive LC/MS, GC/MS, and NMR pipelines using the robust framework. Our pipelines cover the entire spectrum of data analysis, encompassing preprocessing, normalization, quality control, statistical analysis, and annotation steps.

These modular and adaptable workflows are carefully assembled with a combination of established components (such as XCMS and CAMERA packages) and a suite of tools developed by the team members. Our implementation, accessible through a user-friendly web interface, ensures the completeness of parameter settings and reproducibility. Leveraging the advanced capabilities of , we seamlessly integrate components from diverse sources and types.

This integration has facilitated the creation of an extensible Virtual Research Environment (VRE) tailored for metabolomics communities, including platforms and end-users. Our VRE offers preconfigured workflows for newcomers while catering to experts in the field. This collaborative approach not only ensures accessibility but also encourages knowledge-sharing and enhances the overall research experience.

Galaxy

is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

The main features of this platform are:

  • A real benefit to users with results traceability and storage
  • The ability to share results between users/labs/platforms
  • The possibility to use a complete analysis workflow managing environment
  • Interactive step-by-step tutorials called Galaxy training

Citation

Guitton et al. (2017)

Giacomoni et al. (2014)

References

Giacomoni, Franck, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, et al. 2014. “Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.” Bioinformatics 31 (9): 1493–95. https://doi.org/10.1093/bioinformatics/btu813.
Guitton, Yann, Marie Tremblay-Franco, Gildas Le Corguillé, Jean-François Martin, Mélanie Pétéra, Pierrick Roger-Mele, Alexis Delabrière, et al. 2017. “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 93: 89–101. https://doi.org/https://doi.org/10.1016/j.biocel.2017.07.002.