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:

Simon Benateau avatar Simon BenateauSophie Pamerlon avatar Sophie PamerlonOlivier Norvez avatar Olivier Norvezorcid logoYvan Le Bras avatar Yvan Le BrasJean-Baptiste Mihoub avatar Jean-Baptiste MihoubMarie Josse avatar Marie Josseorcid logoWendi Bacon avatar Wendi Baconorcid logoHelena Rasche avatar Helena RascheClara Urfer avatar Clara UrferSoumya Jha avatar Soumya Jhaorcid logoAnkerl Yassine avatar Ankerl Yassineorcid logoClea Siguret avatar Clea Siguretorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoSaskia Hiltemann avatar Saskia HiltemannVerena Moosmann avatar Verena MoosmannMiguel Roncoroni avatar Miguel RoncoroniEric Coissac avatar Eric Coissacorcid logoWolfgang Maier avatar Wolfgang MaierGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnne Fouilloux avatar Anne FouillouxLaura Russell avatar Laura RussellWilliam Durand avatar William DurandTanguy Genthon avatar Tanguy GenthonDominique Pelletier avatar Dominique Pelletierorcid logoBjörn Grüning avatar Björn Grüningorcid logoPauline Seguineau avatar Pauline SeguineauFrédéric Boyer avatar Frédéric Boyerorcid logoBrigida Gallone avatar Brigida GalloneElisa Michon avatar Elisa MichonNajat Amoukou avatar Najat AmoukouNiall Beard avatar Niall Beardorcid logoColine Royaux avatar Coline Royauxorcid logoBérénice Batut avatar Bérénice Batutorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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

References