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.

5 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

73 Tutorials

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

6 Slides

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

6 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

2 Video Recordings

• Ecology / Metabarcoding/eDNA through Obitools 💬 🗣

2 Events

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

Your Contributor Card

GitHub Activity

github Issues Reported

132 Merged Pull Requests

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

• Revise ENA submission tutorial content and structure
  ecology
• Update interactive tool id link in tutorial
  climate
• Update ORGANISATIONS.yaml add Data Terra logo
  template-and-tools
• update output files related to change of column lat and long
  ecology
• Update tutorial.md update column number
  ecology

Reviewed 49 PRs

We love our community reviewing each other's work!

• Add Annotation AI Pipeline tutorial (marine species — Project Moorev)
  imaging
• Add kilian
  template-and-tools
• Small Changes to the Ecoregionalization Tutorial
  template-and-tools
  ecology
• Add PaulineSGN as code owner for ecology topic
  template-and-tools
• Add new tutorial for SAM3
  template-and-tools
  ecology

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