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

Contributors

This material was contributed to by:

orcid logoClea Siguret avatar Clea SiguretElisa Michon avatar Elisa MichonMarie Josse avatar Marie Josseorcid logoWendi Bacon avatar Wendi Baconorcid logoDaniela Schneider avatar Daniela SchneiderSimon Benateau avatar Simon Benateauorcid logoColine Royaux avatar Coline RoyauxMiguel Roncoroni avatar Miguel Roncoroniorcid logoAnkerl Yassine avatar Ankerl YassineClara Urfer avatar Clara UrferElouan Le Mestric avatar Elouan Le MestricTanguy Genthon avatar Tanguy Genthonorcid logoCristóbal Gallardo avatar Cristóbal GallardoNajat Amoukou avatar Najat AmoukouGildas Le Corguillé avatar Gildas Le Corguilléorcid logoNicola Soranzo avatar Nicola SoranzoJean Le Cras avatar Jean Le CrasSophie Pamerlon avatar Sophie PamerlonSoumya Jha avatar Soumya Jhaorcid logoPauline Seguineau avatar Pauline Seguineauorcid logoWolfgang Maier avatar Wolfgang MaierLaura Russell avatar Laura Russellorcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia HiltemannFrédéric Boyer avatar Frédéric BoyerVerena Moosmann avatar Verena Moosmannorcid logoBjörn Grüning avatar Björn GrüningOlivier Norvez avatar Olivier NorvezNiall Beard avatar Niall BeardDominique Pelletier avatar Dominique PelletierWilliam Durand avatar William Durandorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoHelena Rasche avatar Helena RascheJohn Beliveau avatar John BeliveauJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoBrigida Gallone avatar Brigida GalloneEric Coissac avatar Eric Coissacorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoAnne Fouilloux avatar Anne Fouilloux

Funding

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

References