Yvan Le Bras

Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Topic: Foundations of Data Science
• Topic: Ecology
• Topic: Sequence analysis
• Learning Pathway: Introduction to Galaxy and Ecological data analysis
• Learning Pathway: Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery

Tutorials

• Using Galaxy and Managing your Data / RStudio in Galaxy 🧐
• FAIR Data, Workflows, and Research / RO-Crate in Python 🧐
• FAIR Data, Workflows, and Research / Best practices for workflows in GitHub repositories 🧐
• FAIR Data, Workflows, and Research / Exporting Workflow Run RO-Crates from Galaxy 🧐
• FAIR Data, Workflows, and Research / Submitting workflows to LifeMonitor 🧐
• Ecology / Object detection with YOLO ✍️ 🧐
• Ecology / QGIS Web Feature Services ✍️ 🧐
• Ecology / Biodiversity data exploration ✍️ 🧐
• Ecology / Visualize EBV cube data with Panoply netCDF viewer ✍️ 🧐
• Ecology / Life Traits Ecoregionalization workflow ✍️ 🧐
• Ecology / RAD-Seq to construct genetic maps ✍️ 🧐
• Ecology / Metabarcoding/eDNA through Obitools ✍️ 🧐
• Ecology / Cleaning GBIF data for the use in Ecology ✍️ 🧐
• Ecology / Audio data annotation with NEAL (Nature + Energy Audio labeler) ✍️ 🧐
• Ecology / Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities ✍️ 📝 🧐
• Ecology / Taxonomic Analysis of eDNA 🧐
• Ecology / Cleaning GBIF data using OpenRefine ✍️ 🧐
• Ecology / Phylodiversity analysis quick tutorial ✍️ 🧐
• Ecology / Ecoregionalization workflow tutorial ⚙️ 🧐
• Ecology / RAD-Seq Reference-based data analysis ✍️ 🧐
• Ecology / Sentinel 2 biodiversity ✍️ 🧐
• Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite ✍️ 🧐
• Ecology / Regional GAM ✍️ 🧐
• Ecology / Data submission using ENA upload Tool ✍️ ⚙️ 🧐
• Ecology / Species distribution modeling ✍️ 🧐
• Ecology / RAD-Seq de-novo data analysis ✍️ 🧐
• Ecology / Champs blocs indicators ✍️ 🧐
• Ecology / Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS ✍️ 📝
• Ecology / SAM3 – AI-based Semantic Segmentation of marine biodiversity Images and Videos ✍️ 🧐
• Ecology / Obis marine indicators ✍️ 🧐
• Development in Galaxy / nb2workflow: Generating Galaxy Tools From Jupyter Notebooks 🧐
• Development in Galaxy / Galaxy Interactive Tools ✍️
• Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
• Galaxy Server administration / Galaxy Monitoring with Reports 🧐
• Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools 🧐
• Climate / Visualize Climate data with Panoply netCDF viewer 🧐
• Climate / Pangeo Notebook in Galaxy - Introduction to Xarray 🧐
• Epigenetics / ATAC-Seq data analysis 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
• Ecology / Production d'indicateurs champs de bloc ✍️ 🧐
• Ecology / SAM3 – Segmentation sémantique d'images et de vidéos via IA ✍️ 🧐

Slides

• Variant Analysis / Introduction to Variant analysis ✍️
• Galaxy Server administration / Server: Other 🧐
• Climate / Pangeo ecosystem 101 for everyone 🧐
• Climate / The Pangeo ecosystem 🧐
• Assembly / De Bruijn Graph Assembly 🧐
• Epigenetics / Introduction to DNA Methylation data analysis ✍️

FAQs

• It says I already have an account when registering for ecology.usegalaxy.eu
• Changer le type de données
• Importer via un lien
• Créer un nouvel history
• Launch RStudio
• Stop RStudio

Video Recordings

• Ecology / Metabarcoding/eDNA through Obitools 💬 🗣

Events

• Galaxy Ecology training and collabroation fest 🎪
• Galaxy Training Academy 2026 🧑‍🏫

GitHub Activity

github Issues Reported

125 Merged Pull Requests

See all of the github Pull Requests and github Commits by Yvan Le Bras.

• Update tutorial.md correct typo
  ecology
• Update metadata.yaml Clean ecology topics training section
  ecology
• Create tutorial.md yolo detection marine ecology
  template-and-tools
  ecology
• Update tutorial.md modify subsection and add level
  ecology
• Update tutorial.md add level
  ecology

Reviewed 46 PRs

We love our community reviewing each other's work!

• Add PaulineSGN as code owner for ecology topic
  template-and-tools
• Add new tutorial for SAM3
  template-and-tools
  ecology
• Create tutorial.md yolo detection marine ecology
  template-and-tools
  ecology
• Update Estamp URL
  ecology
• Initiate Galaxy Ecology november event 2025-11-11
  template-and-tools

News

External Links

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