Marius van den Beek

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.

67 Tutorials

• Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step 🧐
• Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis ✍️
• Foundations of Data Science / Variant Calling Workflow 🧐
• Foundations of Data Science / Conda Environments For Software Development 🧐
• Foundations of Data Science / Advanced SQL 🧐
• Foundations of Data Science / Python - Multiprocessing 🧐
• Foundations of Data Science / Version Control with Git 🧐
• Foundations of Data Science / R basics in Galaxy 🧐
• Foundations of Data Science / Virtual Environments For Software Development 🧐
• Foundations of Data Science / Python - Argparse 🧐
• Foundations of Data Science / Python - Testing 🧐
• Foundations of Data Science / Advanced R in Galaxy 🧐
• Foundations of Data Science / Plotting in Python 🧐
• Foundations of Data Science / Introduction to SQL 🧐
• Foundations of Data Science / SQL with R 🧐
• Foundations of Data Science / SQL with Python 🧐
• Foundations of Data Science / Python - Type annotations 📝 🧐
• Foundations of Data Science / Basics of using Git from the Command Line 🧐
• Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
• Contributing to the Galaxy Training Material / Teaching Python 🧐
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment 🧐
• Development in Galaxy / Debugging Galaxy 🧐
• Development in Galaxy / Galaxy Interactive Tools 🧐
• Single Cell / Clustering 3K PBMCs with Scanpy 🧐
• Galaxy Server administration / Performant Uploads with TUS ✍️ 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
• Galaxy Server administration / Enable upload via FTP 🧐
• Galaxy Server administration / Automation with Jenkins 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 📝 🧐
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar ✍️ 🧐
• Galaxy Server administration / Setting up Celery Workers for Galaxy 🧐
• Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐
• Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
• Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
• Galaxy Server administration / Galaxy Tool Management with Ephemeris 🧐
• Galaxy Server administration / Deploying a Beacon v1 in Galaxy 🧐
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐
• Galaxy Server administration / Galaxy Monitoring with Reports 🧐
• Galaxy Server administration / External Authentication 🧐
• Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
• Galaxy Server administration / Distributed Object Storage 🧐
• Galaxy Server administration / Data Libraries 🧐
• Galaxy Server administration / Monitoring Galaxy and Pulsar with Sentry ✍️ 🧐
• Galaxy Server administration / Reference Data with CVMFS 🧐
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs ✍️ 🧐
• Introduction to Galaxy Analyses / NGS data logistics ✍️
• Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
• Imaging / Quantitative Analysis of Histological Staining Using Color Deconvolution 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis 🧐
• Transcriptomics / Differential abundance testing of small RNAs 🧐
• Using Galaxy and Managing your Data / Workflow Reports 🖥
• Using Galaxy and Managing your Data / Searching Your History 🧐
• Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows ✍️
• Using Galaxy and Managing your Data / Using Workflow Parameters ✍️ 🧐
• Using Galaxy and Managing your Data / Group tags for complex experimental designs ✍️ 🧐
• Using Galaxy and Managing your Data / Rule Based Uploader 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐

7 Slides

• Development in Galaxy / Scripting Galaxy using the API and BioBlend 🧐
• Galaxy Server administration / uWSGI 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar ✍️
• Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐

1 FAQ

• Debugging Memory Leaks

2 Video Recordings

• Using Galaxy and Managing your Data / Using Workflow Parameters 💬 🗣

2 Events

• 2023 Galaxy Admin Training (Ghent) 🧑‍🏫
• 2025 Galaxy Admin Training (Brno) 🧑‍🏫

Your Contributor Card

GitHub Activity

github Issues Reported

42 Merged Pull Requests

See all of the github Pull Requests and github Commits by Marius van den Beek.

• Fix reference to interactivetools_map
  admin
• Update sentry tutorial
  admin
• Remove one more duplicate subtopic key
  fair
• Fix GTN deployment, remove duplicate subtopic key
  fair
• Add setuptools pulsar requirement and drop amqp pin
  admin

Reviewed 37 PRs

We love our community reviewing each other's work!

• New tutorial: Quantitative Analysis of Histological Staining Using Color Deconvolution
  imaging
• [GAT] Update Galaxy Interactive Tools tutorial and slides
  admin
• add the /cvmfs/data.galaxyproject.org to the singularity volumes
  admin
• [GAT] Fix slurm and tpv trainings
  admin
• [GAT] adjust admin path FAQ for gatbrno schedule
  admin

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