Ecology

Learn to analyse Ecological data through Galaxy.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

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

Material

Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
Biodiversity data exploration tutorial
  • Cleaning GBIF data for the use in Ecology tutorial
    Compute and analyze biodiversity metrics with PAMPA toolsuite tutorial
  • Metabarcoding/eDNA through Obitools tutorial
  • Preparing genomic data for phylogeny reconstruction tutorial
    RAD-Seq de-novo data analysis tutorial
    RAD-Seq Reference-based data analysis tutorial
    RAD-Seq to construct genetic maps tutorial
    Regional GAM tutorial
    Species distribution modeling tutorial
    Visualization of Climate Data using NetCDF xarray Map Plotting tutorial
    Visualize EBV cube data with Panoply netCDF viewer tutorial

    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/ecology-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 password to access everything.

    Frequently Asked Questions

    Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

    Maintainers

    This material is maintained by:

    orcid logoAvatarYvan Le Bras

    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:

    AvatarOlivier NorvezAvatarMarie Josseorcid logoAvatarColine Royauxorcid logoAvatarYvan Le BrasAvatarSimon BenateauAvatarJean-Baptiste MihoubAvatarEric CoissacAvatarFrédéric BoyerAvatarMiguel Roncoroniorcid logoAvatarBrigida GalloneAvatarClara UrferAvatarElisa Michonorcid logoAvatarBérénice BatutAvatarSoumya JhaAvatarAnne Fouilloux

    References