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: Data analysis and modelling for evidence and hypothesis generation and knowledge discovery

73 Tutorials

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

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

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

134 Merged Pull Requests

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

• correct typos and propose an enhencement
  genome-annotation
• 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

Reviewed 50 PRs

We love our community reviewing each other's work!

• fix topic names
  genome-annotation
  galaxy-interface
  computational-chemistry
  ecology
  imaging
• 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

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