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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Thursday, June 29 • 14:40 - 15:00
Workflow4Metabolomics: Towards an international computing infrastructure and a tools showcase for Metabolomics

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Slides

Authors

  • Gildas Le Corguillé, ABiMS
  • Franck Giacomoni, PFEM
  • Pierrick Roger-Mele, Laboratory for Data Analysis and Systems Intelligence (CEA-LIST/LADIS)  
  • Christophe Duperier, PFEM  
  • Mélanie Pétéra, PFEM  
  • Yann Guitton, Laboratoire d'Etude des Résidus et Contaminants dans les Aliments - Oniris (LABERCA)  
  • Marie Tremblay-Franco, Toxalim  
  • Jean-François Martin, Toxalim  
  • Cécile Canlet, Toxalim  
  • Alexis Delabrière, Laboratory for Data Analysis and Systems Intelligence (CEA-LIST/LADIS)  
  • Etienne Thévenot, Laboratory for Data Analysis and Systems Intelligence (CEA-LIST/LADIS)  
  • Christophe Caron, Ingenum



Abstract
Metabolomics data analysis is a complex, multistep process, which is constantly evolving with the development of new analytical technologies, mathematical methods, and bioinformatics tools and databases. The Workflow4Metabolomics (W4M) project aim to develop full LC/MS, GC/MS, FIA/MS and NMR pipelines using Galaxy framework for data analysis including preprocessing, normalization, quality control, statistical analysis and annotation steps.

The W4M Core Team is fully involved building tools for the metabolomics community and its does particular efforts in tool quality and for disseminate their work. The tools developed strive to adopt recommendations implemented by the Galaxy team and the IUC Best Practices. Wrappers are openly available on GitHub and automatically tested using Planemo on the TravisCI platform. The dependencies are managed with Conda packages. Eventually, wrappers are distributed on the ToolShed. Thanks to the Galaxy community, we are allowed to provide some ready-for-use Docker Galaxy flavor and Vagrant VM using Ansible roles.

Meanwhile, the Workflow4Metabolomics Galaxy infrastructure (workflow4metabolomics.org) provides an on-line, user-friendly and high-performance environment to build, run and share metabolomics workflows for LC-MS, GC-MS,  FIA/MS and NMR technologies. In parallel of providing expert and reference workflows, the W4M infrastructure is totally open to community contributions. This contribution should take different forms: i) as complete integration in the W4M ecosystem, shared input/output formats and support involvement or ii) using W4M portal and infrastructure as a showcase for external developers, proposing a functional version of a tool.


Presenters
avatar for Gildas Le Corguillé

Gildas Le Corguillé

CNRS-UPMC - Station Biologique de Roscoff - ABiMS



Thursday June 29, 2017 14:40 - 15:00
Einstein Auditorium Le Corum, Level 0

Attendees (16)