Ecology

Learn to analyse Ecological data through Galaxy.

Requirements

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

Material

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

Data and Metadata Management

These tutorials are focusing on data and metadata management in Ecology.

Lesson Slides Hands-on Recordings Input dataset Workflows
Cleaning GBIF data using OpenRefine
Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS
Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
Data submission using ENA upload Tool

Data access

These lessons focus on ways to access data classicaly used in Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
QGIS Web Feature Services

Data preprocessing

These lessons focus on manners to preprocess data used in Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Biodiversity data exploration
Checking expected species and contamination in bacterial isolate
Cleaning GBIF data for the use in Ecology

Data analysis

These lessons focus on ways to analyse data in Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Champs blocs indicators
Compute and analyze biodiversity metrics with PAMPA toolsuite
Ecoregionalization workflow tutorial
From NDVI data with OpenEO to time series visualisation with Holoviews
Marine Omics identifying biosynthetic gene clusters
Metabarcoding/eDNA through Obitools
Obis marine indicators
Preparing genomic data for phylogeny reconstruction
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

Data visualization

These tutorials showcase data visualization in Ecology

Lesson Slides Hands-on Recordings Input dataset Workflows
Visualization of Climate Data using NetCDF xarray Map Plotting
Visualize EBV cube data with Panoply netCDF viewer

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

Contributors

This material was contributed to by:

Najat Amoukou avatar Najat AmoukouEric Coissac avatar Eric CoissacTanguy Genthon avatar Tanguy Genthonorcid logoAnkerl Yassine avatar Ankerl Yassineorcid logoClea Siguret avatar Clea Siguretorcid logoBrigida Gallone avatar Brigida Galloneorcid logoBjörn Grüning avatar Björn Grüningorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoHelena Rasche avatar Helena RascheSoumya Jha avatar Soumya JhaWilliam Durand avatar William DurandSimon Benateau avatar Simon Benateauorcid logoAnne Fouilloux avatar Anne FouillouxClara Urfer avatar Clara UrferJean-Baptiste Mihoub avatar Jean-Baptiste MihoubMiguel Roncoroni avatar Miguel Roncoroniorcid logoSaskia Hiltemann avatar Saskia HiltemannDominique Pelletier avatar Dominique PelletierOlivier Norvez avatar Olivier Norvezorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal GallardoSophie Pamerlon avatar Sophie Pamerlonorcid logoYvan Le Bras avatar Yvan Le BrasMarie Josse avatar Marie Josseorcid logoNicola Soranzo avatar Nicola SoranzoElisa Michon avatar Elisa Michonorcid logoWendi Bacon avatar Wendi BaconNiall Beard avatar Niall BeardGildas Le Corguillé avatar Gildas Le CorguilléLaura Russell avatar Laura Russellorcid logoColine Royaux avatar Coline RoyauxFrédéric Boyer avatar Frédéric BoyerVerena Moosmann avatar Verena Moosmann

Funding

These individuals or organisations provided funding support for the development of this resource

References