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:

Frédéric Boyer avatar Frédéric Boyerorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoDaniela Schneider avatar Daniela SchneiderJean-Baptiste Mihoub avatar Jean-Baptiste MihoubVerena Moosmann avatar Verena MoosmannElisa Michon avatar Elisa Michonorcid logoBérénice Batut avatar Bérénice BatutTanguy Genthon avatar Tanguy GenthonWilliam Durand avatar William Durandorcid logoClea Siguret avatar Clea SiguretMarie Josse avatar Marie JosseSoumya Jha avatar Soumya Jhaorcid logoCristóbal Gallardo avatar Cristóbal GallardoClara Urfer avatar Clara Urferorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoBjörn Grüning avatar Björn Grüningorcid logoPauline Seguineau avatar Pauline SeguineauSophie Pamerlon avatar Sophie PamerlonJean Le Cras avatar Jean Le Crasorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoColine Royaux avatar Coline RoyauxNiall Beard avatar Niall Beardorcid logoHelena Rasche avatar Helena Rascheorcid logoBrigida Gallone avatar Brigida GalloneSimon Benateau avatar Simon BenateauDominique Pelletier avatar Dominique PelletierElouan Le Mestric avatar Elouan Le MestricOlivier Norvez avatar Olivier Norvezorcid logoAnkerl Yassine avatar Ankerl Yassineorcid logoAnne Fouilloux avatar Anne FouillouxGildas Le Corguillé avatar Gildas Le CorguilléMiguel Roncoroni avatar Miguel RoncoroniJohn Beliveau avatar John BeliveauLaura Russell avatar Laura Russellorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoWendi Bacon avatar Wendi BaconNajat Amoukou avatar Najat Amoukouorcid logoSaskia Hiltemann avatar Saskia HiltemannEric Coissac avatar Eric Coissac

Funding

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

References