Teresa Müller

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: Using Galaxy and Managing your Data
• Topic: Introduction to Galaxy Analyses

Tutorials

• Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
• Introduction to Galaxy Analyses / From peaks to genes 📝
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Introduction to Galaxy Analyses / NGS data logistics 🧐
• Contributing to the Galaxy Training Material / Preview the GTN website as you edit your training material 📝
• Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy 📝 🧐
• Using Galaxy and Managing your Data / JupyterLab in Galaxy 📝 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
• Single Cell / Clustering 3K PBMCs with Scanpy 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) 🧐
• Single Cell / Generating a single cell matrix using Alevin 🧐
• Single Cell / Clustering 3K PBMCs with Seurat 🧐
• Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data 🧐
• Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease 🧐
• Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing ✍️ 🧐
• Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data 🧐
• Microbiome / Calculating α and β diversity from microbiome taxonomic data 🧐
• Microbiome / Binning of metagenomic sequencing data 🧐
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot 🧐
• Statistics and machine learning / Fine tune large protein model (ProtTrans) using HuggingFace 🧐
• Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) 🧐
• Statistics and machine learning / Basics of machine learning 🧐
• Statistics and machine learning / Regression in Machine Learning 🧐
• Statistics and machine learning / Building the LORIS LLR6 PanCancer Model Using PyCaret 🧐
• Statistics and machine learning / Classification in Machine Learning 🧐
• Assembly / Assembly of the mitochondrial genome from PacBio HiFi reads 🧐
• Assembly / ERGA post-assembly QC 🧐
• Assembly / Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data 🧐
• Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data 🧐
• Assembly / Chloroplast genome assembly 🧐
• Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data 🧐
• Sequence analysis / Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants 🧐
• Sequence analysis / Mapping 🧐
• Sequence analysis / Quality Control 🧐
• Genome Annotation / Long non-coding RNAs (lncRNAs) annotation with FEELnc 🧐
• Genome Annotation / Bacterial Genome Annotation 🧐
• Climate / Collaboration with JupyterGIS 🧐
• Digital Humanities / Text-Mining Differences in Chinese Newspaper Articles 🧐
• Foundations of Data Science / One protein along the UniProt page 🧐
• Foundations of Data Science / Learning about one gene across biological resources and formats ✍️ 🧐

Slides

• Single Cell / Single-cell Formats and Resources 🧐
• Statistics and machine learning / Fine-tuning Protein Language Model 🧐
• Statistics and machine learning / Introduction to Machine learning 🧐
• Statistics and machine learning / Regression in Machine Learning 🧐
• Statistics and machine learning / Classification in Machine Learning 🧐

FAQs

• How do I re-use equivalent jobs in Galaxy (aka Job Cache)?

Video Recordings

• Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy 💬 🗣

Events

• Workshop on high-throughput sequencing data analysis with Galaxy 🧑‍🏫
• A practical introduction to bioinformatics and RNA-seq using Galaxy 🎪 🧑‍🏫
• From zero to hero with Python 🎪
• BioNT Community Event & CarpentryConnect - Heidelberg 2024 🎪
• An introduction to High Performance Computing 🎪
• Code & Collaborate: The FAIRytale of Software Development 🎪
• Awareness in Data Management and Analysis for Industry and Research 🎪
• Workshop on high-throughput sequencing data analysis with Galaxy 🎪 🧑‍🏫
• Galaxy Training Academy 2025 🎪 🧑‍🏫
• From Data to Discovery: Metagenomics, RNA-Seq - NGS Bioinformatics with Galaxy 🎪 🧑‍🏫
• Galaxy Training Academy 2024 🎪 🧑‍🏫

GitHub Activity

github Issues Reported

49 Merged Pull Requests

See all of the github Pull Requests and github Commits by Teresa Müller.

• Data olympics update based on comments of the GTA
  introduction
  faqs
• updated FAQ on collection
  microbiome
  GTA
• updated registration date
  template-and-tools
• updated people who signed up for Slack support
  template-and-tools
• Update gta page
  template-and-tools

Reviewed 69 PRs

We love our community reviewing each other's work!

• update contributors for Teresa and Lisanna
  template-and-tools
  digital-humanities
• Remove mention of tabular file containing estimators' hyperparameters
  statistics
• Create news item for Galaxy Workshop promotion 2025-05-12_Galaxy_WS_Freiburg
  news
• Update gta2025-ml.md
  template-and-tools
• Update model output format and tool's versions
  statistics

News

External Links

Favourite Topics

Favourite Formats