Marie Josse

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.

4 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: Earth Data science
• Topic: Ecology
• Learning Pathway: Discovering Galaxy through climate analysis
• Learning Pathway: Tool development for a nice & shiny subdomain

60 Tutorials

• Development in Galaxy / Galaxy Interactive Tools ✍️ 🧐
• Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
• FAIR Data, Workflows, and Research / Exporting Workflow Run RO-Crates from Galaxy 📝 🧐
• Earth Data science / Ocean's variables study ✍️ 🧐
• Earth Data science / Sentinel 5P data visualisation ✍️
• Earth Data science / Analyse Argo data ✍️ 🧐
• Earth Data science / Ocean Data View (ODV) ✍️ 🧐
• Earth Data science / Nitrate DMQC for autonomous platforms such as Argo floats ✍️ 🧐
• Earth Data science / Getting your hands-on earth data ✍️ 🧐
• Ecology / Biodiversity data exploration ✍️
• Ecology / Ecoregionalization workflow tutorial ⚙️
• Ecology / Object detection with YOLO ⚙️ 🧐
• Ecology / Life Traits Ecoregionalization workflow 🧐
• Ecology / Phylodiversity analysis quick tutorial 🧐
• Ecology / RAD-Seq to construct genetic maps 🧐
• Ecology / SAM3 – AI-based Semantic Segmentation of marine biodiversity Images and Videos 🧐
• Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite 🧐
• Ecology / RAD-Seq Reference-based data analysis 🧐
• Ecology / QGIS Web Feature Services ✍️ 🧐
• Ecology / Data submission using ENA upload Tool 🧐
• Ecology / Cleaning GBIF data using OpenRefine 🧐
• Ecology / Metabarcoding/eDNA through Obitools 🧐
• Ecology / Taxonomic Analysis of eDNA 🧐
• Ecology / Species distribution modeling 🧐
• Ecology / Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities 🧐
• Ecology / Visualize EBV cube data with Panoply netCDF viewer ✍️ 🧐
• Ecology / Sentinel 2 biodiversity ✍️
• Ecology / Champs blocs indicators ✍️ 🧐
• Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews ✍️ 🧐
• Ecology / Marine Omics identifying biosynthetic gene clusters ✍️
• Ecology / RAD-Seq de-novo data analysis 🧐
• Ecology / Obis marine indicators ✍️ 🧐
• Ecology / Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS 🧐
• Ecology / Regional GAM 🧐
• Galaxy Server administration / Adding file-sources to Galaxy ✍️
• Galaxy Server administration / Create a subdomain for your community on UseGalaxy.eu ✍️ 🧐
• Galaxy Community Building / Make your tools available on your subdomain ✍️ 🧐
• Galaxy Community Building / Creation of resources listing Galaxy workflow for your community 🧐
• Galaxy Community Building / Creation of the labs in the different Galaxy instances for your community 🧐
• Galaxy Community Building / Creation of resources listing all the tools and their metadata relevant to your community 🧐
• Galaxy Community Building / Creation of a Galaxy tutorial table for your community 🧐
• Imaging / AI pipeline for annotating marine species (Project Moorev - Marine) 🧐
• Ecology / SAM3 – Segmentation sémantique d'images et de vidéos via IA 🧐
• Ecology / Production d'indicateurs champs de bloc ✍️
• Imaging / Pipeline d'annotation d'espèces marines par IA (Project Moorev - Marine) 🧐

1 Slide

• FAIR Data, Workflows, and Research / An earth-system RO-Crate ✍️

2 FAQs

• Creating a dataset collection with autobuild
• Running a workflow

Your Contributor Card

GitHub Activity

github Issues Reported

33 Merged Pull Requests

See all of the github Pull Requests and github Commits by Marie Josse.

• Category
  climate
• Update marie's affiliations
  template-and-tools
• Add kilian
  template-and-tools
• add letter a-e in text
  faqs
• Review community tuto

Reviewed 23 PRs

We love our community reviewing each other's work!

• Revise ENA submission tutorial content and structure
  ecology
• Add Annotation AI Pipeline tutorial (marine species — Project Moorev)
  imaging
• Update metadata.yaml Clean ecology topics training section
  ecology
• Create tutorial.md yolo detection marine ecology
  template-and-tools
  ecology
• Add new tutorial for SAM3
  template-and-tools
  ecology

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