Peter van Heusden

Research at the South African National Bioinformatics Institute

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.

• Evolution
• One Health

Tutorials

• Galaxy Server administration / Galaxy Installation with Ansible 🧐
• Evolution / Tree thinking for tuberculosis evolution and epidemiology 🧐
• Evolution / Identifying tuberculosis transmission links: from SNPs to transmission clusters 🧐
• Contributing to the Galaxy Training Material / Teaching Python 🧐
• Foundations of Data Science / Advanced R in Galaxy 🧐
• Foundations of Data Science / Conda Environments For Software Development 🧐
• Foundations of Data Science / SQL with R 🧐
• Foundations of Data Science / Python - Type annotations 📝 🧐
• Foundations of Data Science / Advanced SQL 🧐
• Foundations of Data Science / Virtual Environments For Software Development 🧐
• Foundations of Data Science / Python - Testing 🧐
• Foundations of Data Science / Python - Multiprocessing 🧐
• Foundations of Data Science / Python - Argparse 🧐
• Foundations of Data Science / R basics in Galaxy 🧐
• Foundations of Data Science / Version Control with Git 🧐
• Foundations of Data Science / Variant Calling Workflow 🧐
• Foundations of Data Science / Basics of using Git from the Command Line 🧐
• Foundations of Data Science / Plotting in Python 🧐
• Foundations of Data Science / Introduction to SQL 🧐
• Foundations of Data Science / SQL with Python 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️
• Variant Analysis / M. tuberculosis Variant Analysis ✍️ 🧐
• Variant Analysis / Microbial Variant Calling 🧐
• Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐

FAQs

• TB Variant Report crashes (with an error about KeyError: 'protein')
• My snippy is running for a very long time. Is this normal?
• Do I have to run the tools in the order of the tutorial?
• Opening the workflow editor

Video Recordings

• Sequence analysis / Mapping 🗣
• Sequence analysis / Mapping 🗣
• Variant Analysis / M. tuberculosis Variant Analysis 💬 🗣

Events

• Mycobacterium tuberculosis complex NGS made easy 🎪 🧑‍🏫

GitHub Activity

github Issues Reported

27 Merged Pull Requests

See all of the github Pull Requests and github Commits by Peter van Heusden.

• Correct title for Mycobacterium tuberculosis NGS made easy blog post
  news
• Update: TB Variant Analysis: Add alternative instructions on importing the workflow into Galaxy
  variant-analysis
• Update tb variant analysis tutorial: fix some numbers
  variant-analysis
• Updates to TB variant analysis tutorial
  review-needed
  variant-analysis
  template-and-tools
• TB Variant Analysis: Update tb_variant_filter to v. 0.4.0
  variant-analysis

Reviewed 10 PRs

We love our community reviewing each other's work!

• Updates to TB variant analysis tutorial
  review-needed
  variant-analysis
  template-and-tools
• ABCD python level 2 for avans
• Add canonical headers to training materials, decreasing indexing of proxies.
• Add key error faq
• MTB phylogenetics tutorial

News

External Links

Favourite Topics

Favourite Formats