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:

Olivier Norvez avatar Olivier Norvezorcid logoGlinez Thibaud avatar Glinez ThibaudFrédéric Boyer avatar Frédéric BoyerNajat Amoukou avatar Najat Amoukouorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoBjörn Grüning avatar Björn GrüningSophie Pamerlon avatar Sophie Pamerlonorcid logoAnne Fouilloux avatar Anne FouillouxElisa Michon avatar Elisa MichonEric Coissac avatar Eric CoissacNiall Beard avatar Niall BeardDominique Pelletier avatar Dominique PelletierWilliam Durand avatar William Durandorcid logoBérénice Batut avatar Bérénice BatutElouan Le Mestric avatar Elouan Le MestricVerena Moosmann avatar Verena Moosmannorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoHelena Rasche avatar Helena Rascheorcid logoPauline Seguineau avatar Pauline SeguineauClara Urfer avatar Clara UrferLaura Russell avatar Laura Russellorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le Corguilléorcid logoClea Siguret avatar Clea SiguretMarie Josse avatar Marie Josseorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoSaskia Hiltemann avatar Saskia HiltemannMiguel Roncoroni avatar Miguel RoncoroniJean Le Cras avatar Jean Le CrasSimon Benateau avatar Simon Benateauorcid logoColine Royaux avatar Coline RoyauxSoumya Jha avatar Soumya JhaJohn Beliveau avatar John BeliveauTanguy Genthon avatar Tanguy Genthonorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnkerl Yassine avatar Ankerl YassineJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoBrigida Gallone avatar Brigida Galloneorcid logoWendi Bacon avatar Wendi Bacon

Funding

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

References