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
Life Traits Ecorgionalization workflow
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
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:

Niall Beard avatar Niall Beardorcid logoWendi Bacon avatar Wendi BaconFrédéric Boyer avatar Frédéric BoyerSoumya Jha avatar Soumya Jhaorcid logoAnne Fouilloux avatar Anne Fouillouxorcid logoHelena Rasche avatar Helena Rascheorcid logoBérénice Batut avatar Bérénice BatutGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBjörn Grüning avatar Björn Grüningorcid logoDaniela Schneider avatar Daniela Schneiderorcid logoBrigida Gallone avatar Brigida GalloneMarie Josse avatar Marie Josseorcid logoClea Siguret avatar Clea SiguretNajat Amoukou avatar Najat AmoukouElisa Michon avatar Elisa MichonClara Urfer avatar Clara Urferorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoGlinez Thibaud avatar Glinez ThibaudTanguy Genthon avatar Tanguy GenthonJohn Beliveau avatar John Beliveauorcid logoAnkerl Yassine avatar Ankerl YassineSophie Pamerlon avatar Sophie Pamerlonorcid logoColine Royaux avatar Coline RoyauxLaura Russell avatar Laura Russellorcid logoNicola Soranzo avatar Nicola SoranzoWilliam Durand avatar William DurandSimon Benateau avatar Simon Benateauorcid logoCristóbal Gallardo avatar Cristóbal GallardoJean Le Cras avatar Jean Le CrasMiguel Roncoroni avatar Miguel RoncoroniJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoPauline Seguineau avatar Pauline Seguineauorcid logoYvan Le Bras avatar Yvan Le BrasEric Coissac avatar Eric CoissacDominique Pelletier avatar Dominique Pelletierorcid logoWolfgang Maier avatar Wolfgang MaierOlivier Norvez avatar Olivier NorvezVerena Moosmann avatar Verena Moosmann

Funding

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

References