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

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Audio data annotation with NEAL (Nature + Energy Audio labeler).

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:

orcid logoAnne Fouilloux avatar Anne FouillouxJean Le Cras avatar Jean Le CrasGildas Le Corguillé avatar Gildas Le Corguilléorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoHelena Rasche avatar Helena RascheSimon Benateau avatar Simon BenateauNiall Beard avatar Niall BeardClara Urfer avatar Clara Urferorcid logoClea Siguret avatar Clea SiguretDominique Pelletier avatar Dominique Pelletierorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnkerl Yassine avatar Ankerl YassineSophie Pamerlon avatar Sophie PamerlonMiguel Roncoroni avatar Miguel RoncoroniNajat Amoukou avatar Najat AmoukouElouan Le Mestric avatar Elouan Le Mestricorcid logoBjörn Grüning avatar Björn GrüningOlivier Norvez avatar Olivier Norvezorcid logoBérénice Batut avatar Bérénice BatutWilliam Durand avatar William DurandTanguy Genthon avatar Tanguy Genthonorcid logoColine Royaux avatar Coline RoyauxVerena Moosmann avatar Verena MoosmannJohn Beliveau avatar John Beliveauorcid logoGlinez Thibaud avatar Glinez ThibaudElisa Michon avatar Elisa MichonLaura Russell avatar Laura Russellorcid logoBrigida Gallone avatar Brigida Galloneorcid logoYvan Le Bras avatar Yvan Le BrasMarie Josse avatar Marie JosseSoumya Jha avatar Soumya JhaJean-Baptiste Mihoub avatar Jean-Baptiste Mihouborcid logoPauline Seguineau avatar Pauline Seguineauorcid logoWendi Bacon avatar Wendi BaconEric Coissac avatar Eric CoissacFrédéric Boyer avatar Frédéric Boyerorcid logoNicola Soranzo avatar Nicola SoranzoHaswane Chei avatar Haswane Cheiorcid logoDaniela Schneider avatar Daniela Schneider

Funding

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

References