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:

Clara Urfer avatar Clara UrferDominique Pelletier avatar Dominique Pelletierorcid logoBérénice Batut avatar Bérénice BatutJean Le Cras avatar Jean Le Crasorcid logoBjörn Grüning avatar Björn GrüningGildas Le Corguillé avatar Gildas Le Corguilléorcid logoNicola Soranzo avatar Nicola SoranzoJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoBrigida Gallone avatar Brigida GalloneNajat Amoukou avatar Najat Amoukouorcid logoPauline Seguineau avatar Pauline SeguineauElouan Le Mestric avatar Elouan Le Mestricorcid logoClea Siguret avatar Clea SiguretFrédéric Boyer avatar Frédéric Boyerorcid logoAnkerl Yassine avatar Ankerl YassineSophie Pamerlon avatar Sophie Pamerlonorcid logoSaskia Hiltemann avatar Saskia HiltemannElisa Michon avatar Elisa MichonJohn Beliveau avatar John BeliveauOlivier Norvez avatar Olivier Norvezorcid logoDaniela Schneider avatar Daniela SchneiderSimon Benateau avatar Simon Benateauorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoYvan Le Bras avatar Yvan Le BrasWilliam Durand avatar William Durandorcid logoWolfgang Maier avatar Wolfgang MaierEric Coissac avatar Eric Coissacorcid logoHelena Rasche avatar Helena Rascheorcid logoColine Royaux avatar Coline RoyauxTanguy Genthon avatar Tanguy GenthonVerena Moosmann avatar Verena Moosmannorcid logoAnne Fouilloux avatar Anne FouillouxMarie Josse avatar Marie JosseSoumya Jha avatar Soumya Jhaorcid logoWendi Bacon avatar Wendi Baconorcid logoGlinez Thibaud avatar Glinez ThibaudMiguel Roncoroni avatar Miguel RoncoroniNiall Beard avatar Niall BeardLaura Russell avatar Laura Russell

Funding

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

References