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
Biodiversity data exploration
Champs blocs indicators
Checking expected species and contamination in bacterial isolate
Cleaning GBIF data for the use in Ecology
Compute and analyze biodiversity metrics with PAMPA toolsuite
Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
From NDVI data with OpenEO to time series visualisation with Holoviews
Metabarcoding/eDNA through Obitools
Obis marine indicators
Preparing genomic data for phylogeny reconstruction
QGIS Web Feature Services
RAD-Seq Reference-based data analysis
RAD-Seq de-novo data analysis
RAD-Seq to construct genetic maps
Regional GAM
Sentinel 2 biodiversity
Species distribution modeling
Visualization of Climate Data using NetCDF xarray Map Plotting
Visualize EBV cube data with Panoply netCDF viewer

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.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoYvan Le Bras avatar Yvan 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:

Marie Josse avatar Marie JosseJean-Baptiste Mihoub avatar Jean-Baptiste MihoubDominique Pelletier avatar Dominique Pelletierorcid logoHelena Rasche avatar Helena RascheClea Siguret avatar Clea SiguretElisa Michon avatar Elisa MichonOlivier Norvez avatar Olivier NorvezClara Urfer avatar Clara UrferPôle National de Données de Biodiversité avatar Pôle National de Données de Biodiversitéorcid logoColine Royaux avatar Coline Royauxorcid logoYvan Le Bras avatar Yvan Le BrasFrédéric Boyer avatar Frédéric Boyerorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoAnne Fouilloux avatar Anne FouillouxSimon Benateau avatar Simon BenateauSoumya Jha avatar Soumya JhaTanguy Genthon avatar Tanguy GenthonMiguel Roncoroni avatar Miguel Roncoroniorcid logoBérénice Batut avatar Bérénice BatutEric Coissac avatar Eric Coissacorcid logoBrigida Gallone avatar Brigida Gallone

Funders

This material was funded by:

OpenMetaPaper avatar FNSOEuroScienceGateway avatar EuroScienceGatewayABRomics avatar ABRomicsFair-Ease avatar Fair-EaseGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries

References