Metabolomics

Training material to analyse Mass spectrometry data in Galaxy: Metabolomics (LCMS, FIAMS, GCMS, NMR) and imaging.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to Metabolomics
slides
Mass spectrometry imaging: Examining the spatial distribution of analytes
level level level
tutorial zenodo_link workflow
Mass spectrometry imaging: Finding differential analytes
level level level
tutorial zenodo_link workflow
Mass spectrometry: LC-MS analysis
tutorial zenodo_link workflow

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/metabolomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password admin to access everything.

Maintainers

This material is maintained by:

Gildas Le CorguilléGildas Le Corguillé, Mélanie PeteraMélanie Petera, Melanie FöllMelanie Föll

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Gildas Le CorguilléGildas Le Corguillé, Cécile CanletCécile Canlet, Melanie FöllMelanie Föll, Mélanie PeteraMélanie Petera, Jean-François MartinJean-François Martin, Yann GuittonYann Guitton, Workflow4Metabolomics core teamWorkflow4Metabolomics core team