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

Slides

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

GitHub Activity

github Issues Reported

116 Merged Pull Requests

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

• Update tutorial.md aexample apiKey
  ecology
• Update metadata.yaml to add media annotation subsection
  ecology
• Initiate Galaxy Ecology november event 2025-11-11
  template-and-tools
• Update metadata.yaml to add Galaxy Ecology ref & data access and mngt
  ecology
• Update tutorial.md fix typo.. on the title...
  ecology

Reviewed 43 PRs

We love our community reviewing each other's work!

• Update Estamp URL
  ecology
• Initiate Galaxy Ecology november event 2025-11-11
  template-and-tools
• Add some correction in Neal tutorial
  ecology
• Add NEAL tutorial
  template-and-tools
  ecology
• nb2workflow - jupyter nb to galaxy tool training / tutorial
  dev
  template-and-tools

News

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