Ecology

Learn to access, manage and 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
Life Traits Ecoregionalization workflow
Marine Omics identifying biosynthetic gene clusters
Metabarcoding/eDNA through Obitools
Obis marine indicators
Phylodiversity analysis quick tutorial
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
Taxonomic Analysis of eDNA

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

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoYvan Le Bras avatar Yvan Le Bras

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Contributors

This material was contributed to by:

Elisa Michon avatar Elisa Michonorcid logoSaskia Hiltemann avatar Saskia HiltemannElouan Le Mestric avatar Elouan Le MestricWilliam Durand avatar William DurandSophie Pamerlon avatar Sophie PamerlonSimon Benateau avatar Simon BenateauNajat Amoukou avatar Najat Amoukouorcid logoAnkerl Yassine avatar Ankerl YassineJean Le Cras avatar Jean Le Crasorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoGlinez Thibaud avatar Glinez ThibaudSoumya Jha avatar Soumya JhaDominique Pelletier avatar Dominique PelletierClara Urfer avatar Clara Urferorcid logoColine Royaux avatar Coline Royauxorcid logoWendi Bacon avatar Wendi Baconorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoBrigida Gallone avatar Brigida GalloneOlivier Norvez avatar Olivier NorvezEric Coissac avatar Eric CoissacNiall Beard avatar Niall BeardVerena Moosmann avatar Verena Moosmannorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoWolfgang Maier avatar Wolfgang MaierTanguy Genthon avatar Tanguy Genthonorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoHelena Rasche avatar Helena RascheGildas Le Corguillé avatar Gildas Le CorguilléFrédéric Boyer avatar Frédéric BoyerJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoClea Siguret avatar Clea SiguretMarie Josse avatar Marie JosseLaura Russell avatar Laura RussellJohn Beliveau avatar John Beliveauorcid logoPauline Seguineau avatar Pauline SeguineauMiguel Roncoroni avatar Miguel Roncoroniorcid logoBjörn Grüning avatar Björn Grüningorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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

References