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

• Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
• Earth Data science / Ocean's variables study ✍️ 🧐
• Earth Data science / Ocean Data View (ODV) ✍️ 🧐
• Earth Data science / Nitrate DMQC for autonomous platforms such as Argo floats ✍️ 🧐
• Earth Data science / Sentinel 5P data visualisation ✍️
• Earth Data science / Getting your hands-on earth data ✍️ 🧐
• Earth Data science / Analyse Argo data ✍️ 🧐
• Imaging / AI pipeline for annotating marine species (Project Moorev - Marine) 🧐
• Ecology / RAD-Seq Reference-based data analysis 🧐
• Ecology / From NDVI data with OpenEO to time series visualisation with Holoviews ✍️ 🧐
• Ecology / Data submission using ENA upload Tool 🧐
• Ecology / RAD-Seq to construct genetic maps 🧐
• Ecology / Champs blocs indicators ✍️ 🧐
• 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 / Marine Omics identifying biosynthetic gene clusters ✍️
• Ecology / Life Traits Ecoregionalization workflow 🧐
• Ecology / Ecoregionalization workflow tutorial ⚙️
• Ecology / Visualize EBV cube data with Panoply netCDF viewer ✍️ 🧐
• Ecology / Regional GAM 🧐
• 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 🧐
• Galaxy Community Building / Creation of a Galaxy tutorial table for your community 🧐
• Galaxy Community Building / Creation of resources listing Galaxy workflow 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 the labs in the different Galaxy instances for your community 🧐
• Galaxy Community Building / Make your tools available on your subdomain ✍️ 🧐
• Galaxy Server administration / Create a subdomain for your community on UseGalaxy.eu ✍️ 🧐
• Galaxy Server administration / Adding file-sources to Galaxy ✍️
• Development in Galaxy / Galaxy Interactive Tools ✍️ 🧐
• FAIR Data, Workflows, and Research / Exporting Workflow Run RO-Crates from Galaxy 📝 🧐
• 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 🧐

1 Slide

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

2 FAQs

• Creating a dataset collection with autobuild
• Running a workflow

2 Events

• Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability 🎪 🧑‍🏫

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GitHub Activity

github Issues Reported

31 Merged Pull Requests

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

• Add kilian
  template-and-tools
• add letter a-e in text
  faqs
• Review community tuto
• Qcv analysis update
  template-and-tools
  climate
  faqs
• Add new earth system tuto on ocean
  climate

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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