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

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

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Contributors

This material was contributed to by:

orcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoColine Royaux avatar Coline RoyauxDominique Pelletier avatar Dominique PelletierElouan Le Mestric avatar Elouan Le Mestricorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoYvan Le Bras avatar Yvan Le BrasSophie Pamerlon avatar Sophie PamerlonGildas Le Corguillé avatar Gildas Le Corguilléorcid logoCristóbal Gallardo avatar Cristóbal GallardoTanguy Genthon avatar Tanguy GenthonMiguel Roncoroni avatar Miguel RoncoroniSoumya Jha avatar Soumya JhaJohn Beliveau avatar John Beliveauorcid logoWendi Bacon avatar Wendi BaconEric Coissac avatar Eric CoissacVerena Moosmann avatar Verena Moosmannorcid logoSaskia Hiltemann avatar Saskia HiltemannWilliam Durand avatar William Durandorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBrigida Gallone avatar Brigida GalloneLaura Russell avatar Laura RussellClara Urfer avatar Clara Urferorcid logoDaniela Schneider avatar Daniela SchneiderFrédéric Boyer avatar Frédéric Boyerorcid logoClea Siguret avatar Clea Siguretorcid logoAnne Fouilloux avatar Anne FouillouxJean Le Cras avatar Jean Le CrasJean-Baptiste Mihoub avatar Jean-Baptiste MihoubNiall Beard avatar Niall BeardSimon Benateau avatar Simon Benateauorcid logoPauline Seguineau avatar Pauline SeguineauNajat Amoukou avatar Najat Amoukouorcid logoHelena Rasche avatar Helena Rascheorcid logoAnkerl Yassine avatar Ankerl YassineElisa Michon avatar Elisa MichonMarie Josse avatar Marie JosseOlivier Norvez avatar Olivier Norvezorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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

References