Matthias Bernt

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.

Tutorials

• Sequence analysis / Quality Control 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment ✍️ 🧐
• Proteomics / Multiomics data analysis using MultiGSEA ✍️
• Using Galaxy and Managing your Data / Group tags for complex experimental designs 🧐
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs ✍️
• Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 📝 🧐
• Single Cell / Inferring single cell trajectories with Monocle3 🧐
• Single Cell / Scanpy Parameter Iterator 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🧐

Slides

• Galaxy Server administration / Galaxy Administrator Time Burden and Technology Usage 🖥

FAQs

• The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?
• Where can I get planemo?

Video Recordings

• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment 💬 🗣
• Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 💬 🗣

Events

• Galaxy Training Academy 2025 🧑‍🏫
• Galaxy Training Academy 2024 🧑‍🏫

GitHub Activity

github Issues Reported

21 Merged Pull Requests

See all of the github Pull Requests and github Commits by Matthias Bernt.

• Add missing reference to MultiGSEA tutorial
  proteomics
• Add tutorial for multigsea
  template-and-tools
  proteomics
  statistics
• Fix percentage
  microbiome
• rename Shared Data to Data
  transcriptomics
  epigenetics
  faqs
  microbiome
• dada2: bit of polishing
  microbiome

Reviewed 8 PRs

We love our community reviewing each other's work!

• Add DADA2 tutorial
  microbiome
• GCC21: Tool dev tutorial updates
  work-in-progress
  dev
• Fix sharing snippet
  introduction
  template-and-tools
  climate
  faqs
  single-cell
• Fix selector for expanding all
  template-and-tools
• group tags tutorial improvements

News

External Links

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