Ecology

Learn to 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
Marine Omics identifying biosynthetic gene clusters
Metabarcoding/eDNA through Obitools
Obis marine indicators
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

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:

Najat Amoukou avatar Najat Amoukouorcid logoBérénice Batut avatar Bérénice BatutLaura Russell avatar Laura Russellorcid logoHelena Rasche avatar Helena RascheMiguel Roncoroni avatar Miguel RoncoroniGildas Le Corguillé avatar Gildas Le Corguilléorcid logoColine Royaux avatar Coline RoyauxSimon Benateau avatar Simon Benateauorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoYvan Le Bras avatar Yvan Le Brasorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnkerl Yassine avatar Ankerl YassineFrédéric Boyer avatar Frédéric BoyerElisa Michon avatar Elisa Michonorcid logoSaskia Hiltemann avatar Saskia HiltemannNiall Beard avatar Niall BeardVerena Moosmann avatar Verena MoosmannWilliam Durand avatar William Durandorcid logoGlinez Thibaud avatar Glinez Thibaudorcid logoWolfgang Maier avatar Wolfgang MaierSoumya Jha avatar Soumya JhaOlivier Norvez avatar Olivier Norvezorcid logoDaniela Schneider avatar Daniela SchneiderClara Urfer avatar Clara UrferSophie Pamerlon avatar Sophie PamerlonJean-Baptiste Mihoub avatar Jean-Baptiste MihoubEric Coissac avatar Eric CoissacTanguy Genthon avatar Tanguy GenthonMarie Josse avatar Marie Josseorcid logoBrigida Gallone avatar Brigida Galloneorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoClea Siguret avatar Clea SiguretDominique Pelletier avatar Dominique Pelletierorcid logoWendi Bacon avatar Wendi Baconorcid logoPauline Seguineau avatar Pauline Seguineau

Funding

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

References