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
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

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:

Miguel Roncoroni avatar Miguel RoncoroniDominique Pelletier avatar Dominique Pelletierorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoBjörn Grüning avatar Björn GrüningSophie Pamerlon avatar Sophie PamerlonSoumya Jha avatar Soumya Jhaorcid logoAnne Fouilloux avatar Anne FouillouxElouan Le Mestric avatar Elouan Le Mestricorcid logoColine Royaux avatar Coline RoyauxSimon Benateau avatar Simon Benateauorcid logoClea Siguret avatar Clea Siguretorcid logoAnkerl Yassine avatar Ankerl YassineJohn Beliveau avatar John Beliveauorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDaniela Schneider avatar Daniela SchneiderJean Le Cras avatar Jean Le Crasorcid logoBrigida Gallone avatar Brigida Galloneorcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoWendi Bacon avatar Wendi BaconOlivier Norvez avatar Olivier NorvezWilliam Durand avatar William DurandElisa Michon avatar Elisa MichonLaura Russell avatar Laura RussellNajat Amoukou avatar Najat Amoukouorcid logoGlinez Thibaud avatar Glinez ThibaudGildas Le Corguillé avatar Gildas Le Corguilléorcid logoWolfgang Maier avatar Wolfgang MaierNiall Beard avatar Niall BeardClara Urfer avatar Clara UrferMarie Josse avatar Marie Josseorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoYvan Le Bras avatar Yvan Le BrasEric Coissac avatar Eric Coissacorcid logoHelena Rasche avatar Helena RascheTanguy Genthon avatar Tanguy GenthonFrédéric Boyer avatar Frédéric BoyerVerena Moosmann avatar Verena MoosmannJean-Baptiste Mihoub avatar Jean-Baptiste Mihoub

Funding

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

References