Galaxy can be used by ecologs to deal with diverse biodiversity data supporting genetics, species, community or ecosystem information.
Publications
Galaxy Ecology founding article "Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology" published in 2025 is accessible in GigaScience, graphical abstract below
What is available?
Tools
Tools for earth data analysis are freely available in the ToolShed, notably in the Ecology repository, which can be installed on any Galaxy server.
If tools are missing or information is not up-to-date in the list, please help us! Contact Yvan or Pauline about it.
Workflows and tutorials
Several curated Galaxy workflows are publicly available for different kinds of biodiversity data analysis. Many of these are accompanied by comprehensive GTN Tutorials that will guide you through the analysis step by step.
Something missing in the list below? Feel free to update the page or reach to us
Data and Metadata Management
These tutorials are focusing on data and metadata management in Ecology
| Target | GTN Tutorial |
|---|---|
| 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
| Target | GTN Tutorial |
|---|---|
| QGIS Web Feature Services | |
| More to come |
Data preprocessing
These lessons focus on manners to preprocess data used in Ecology
| Target | GTN Tutorial |
|---|---|
| Biodiversity data exploration | Biodiversity state of the art |
| Cleaning GBIF data for the use in Ecology |
Media annotation
These lessons focus on manners to preprocess media data (sound, images, videos) used in Ecology
| Target | GTN Tutorial |
|---|---|
| Audio data annotation with NEAL (Nature + Energy Audio labeler) |
Data analysis
These lessons focus on manners to analyze data used in Ecology
From modeling to biodiversity indicators production
A lot of tools and resources were developped for the French BON (Biodiversity Observation Network) EBV (Essential Biodiversity Variables) operationalization pilot, to showcase the use of Galaxy to construct and share models (GAM, GLM, GLMTMB, BRT, ...) and to produce biodiversity metrics, indices and indicators. Here are presented tutorials particularly related to this topic:
| Target | GTN Tutorial |
|---|---|
| Champs blocs indicators | |
| Compute and analyze biodiversity metrics with PAMPA toolsuite | |
| Regional GAM | |
| Ecoregionalization workflow tutorial | |
| Life Traits Ecoregionalization workflow | |
| Species distribution modeling | |
| Obis marine indicators | |
| Phylodiversity analysis quick tutorial | |
| From NDVI data with OpenEO to time series visualisation with Holoviews | |
| Sentinel 2 biodiversity |
From genetics / genomics biodiversity data
Genetics / genomics data represents a particularly specific biodiversity data type. Here are presented tutorials particularly related to these data:
| Target | GTN Tutorial |
|---|---|
| Marine Omics identifying biosynthetic gene clusters | |
| Metabarcoding/eDNA through Obitools | |
| Taxonomic Analysis of eDNA | |
| Preparing genomic data for phylogeny reconstruction | |
| RAD-Seq Reference-based data analysis | |
| RAD-Seq de-novo data analysis | |
| RAD-Seq to construct genetic maps |
From satelite remote sensing biodiversity data
Satelite remote sensing data represents a particularly specific biodiversity data type. Here are presented tutorials particularly related to these data:
| From NDVI data with OpenEO to time series visualisation with Holoviews | | | Sentinel 2 biodiversity | |
From citizen science biodiversity data
Citizen science data represents a particularly specific biodiversity data type. Here are presented tutorials particularly related to these data:
| Champs blocs indicators | | | Compute and analyze biodiversity metrics with PAMPA toolsuite | | | Regional GAM | |
Data visualization
These lessons focus on manners to visualize data used in Ecology
| Target | GTN Tutorial |
|---|---|
| Visualization of Climate Data using NetCDF xarray Map Plotting | |
| Visualize EBV cube data with Panoply netCDF viewer |
A dedicated interface
Two dedicated interfaces with tools and workflows for Biodiversity data analyses can be accessed :
- for all Ecology related topics ecology.usegalaxy.eu
- for Biodiversity genomics biodiversity.usegalaxy.eu
Training material and events
The Galaxy community organizes regularly training events. You can check the event pages here to get the last ones.
How is Galaxy used for biodiversity data analysis?
Projects / Showcases
Below is a list of projects involving members of this community:
| Project | Description |
|---|---|
| CCAMLR | Commission for the Conservation of Antarctic Marine Living Resources |
| GEO BON | Group on Earth Observation Biodiversity Observation Network EBV (Essential Biodiveristy Variables) operationlization pilot |
| GINAMO | Genetic Indicators for NAture MOnitoring |
| MOOREV | Microclimates and tools for observing the responses of living organisms on the seabed through citizen science |
| OFVi | One forest Vision initiative: Protect tropical forests and wetlands |
Join us
Anybody interested in Ecology data analysis in Galaxy is welcome to join Ecology galaxy community! Everybody is Welcome! Don't hesitate to contact us, for example from our usegalaxy.eu Galaxy Ecology Matrix channel.