Simon Gladman

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.

• Learning Pathway: Admin Training Course

Tutorials

• Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Contributing to the Galaxy Training Material / Including a new topic 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
• Genome Annotation / Genome annotation with Prokka ✍️ 🧐
• Teaching and Hosting Galaxy training / Training Infrastructure as a Service 🧐
• Computational chemistry / High Throughput Molecular Dynamics and Analysis 🧐
• Using Galaxy and Managing your Data / Downloading and Deleting Data in Galaxy ✍️
• Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads 🧐
• Assembly / Unicycler Assembly ✍️
• Assembly / An Introduction to Genome Assembly ✍️ 🧐
• Assembly / De Bruijn Graph Assembly ✍️ 🧐
• Galaxy Server administration / Enable upload via FTP 🧐
• Galaxy Server administration / Reference Data with Data Managers ✍️
• Galaxy Server administration / Reference Data with CVMFS ✍️ 🧐
• Galaxy Server administration / Galaxy Installation with Ansible ✍️ 🧐
• Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
• Galaxy Server administration / Upgrading Galaxy ✍️
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar ✍️ 🧐
• Galaxy Server administration / Reference Data with CVMFS without Ansible ✍️ 🧐
• Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
• Galaxy Server administration / Data Libraries 🧐
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Galaxy Database schema 🧐
• Galaxy Server administration / Galaxy Monitoring with Reports ✍️ 🧐
• Galaxy Server administration / Automation with Jenkins 🧐
• Galaxy Server administration / Galaxy Interactive Tools ✍️ 🧐
• Galaxy Server administration / Distributed Object Storage 🧐
• Galaxy Server administration / External Authentication 🧐
• Galaxy Server administration / Performant Uploads with TUS 🧐
• Galaxy Server administration / Galaxy Tool Management with Ephemeris 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
• Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
• Variant Analysis / Microbial Variant Calling ✍️ 🧐
• Variant Analysis / M. tuberculosis Variant Analysis ✍️
• Variant Analysis / Somatic Variant Discovery from WES Data Using Control-FREEC 🧐
• Variant Analysis / Identification of somatic and germline variants from tumor and normal sample pairs 🧐
• Foundations of Data Science / Basics of using Git from the Command Line 🧐

Slides

• Development in Galaxy / Galaxy Webhooks 🧐
• Development in Galaxy / Galaxy Interactive Tours 🧐
• Genome Annotation / Genome annotation with Prokka ✍️
• Assembly / Deeper look into Genome Assembly algorithms ✍️
• Assembly / Unicycler Assembly ✍️
• Assembly / An Introduction to Genome Assembly ✍️
• Assembly / De Bruijn Graph Assembly ✍️
• Galaxy Server administration / Empathy 🧐
• Galaxy Server administration / Galaxy Monitoring ✍️ 🧐
• Galaxy Server administration / Reference Genomes in Galaxy ✍️
• Galaxy Server administration / Reference Data with CVMFS ✍️
• Galaxy Server administration / Galaxy Installation with Ansible ✍️ 🧐
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar ✍️ 🧐
• Galaxy Server administration / Galaxy Monitoring with gxadmin ✍️
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration ✍️ 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐
• Galaxy Server administration / Galaxy on the Cloud ✍️ 🧐
• Galaxy Server administration / Storage Management 🧐
• Galaxy Server administration / uWSGI ✍️ 🧐
• Galaxy Server administration / External Authentication 🧐
• Galaxy Server administration / Server: Other ✍️
• Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️
• Galaxy Server administration / Galactic Database 🧐
• Galaxy Server administration / Galaxy Troubleshooting 🧐
• Galaxy Server administration / Advanced customisation of a Galaxy instance 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana ✍️ 🧐
• Galaxy Server administration / Galaxy from an administrator's point of view 🧐

FAQs

• How do I know what I can do with a role? What variables are available?
• Why does my assembly graph in Bandage look different to the one pictured in the tutorial?
• Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?
• Running more than one round of Pilon polishing
• Can we polish the assembly with long reads too?

Video Recordings

• Assembly / An Introduction to Genome Assembly 🗣
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🗣
• Galaxy Server administration / Reference Data with CVMFS 💬 🗣
• Galaxy Server administration / Upgrading Galaxy 💬 🗣
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🗣 💬
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 💬 🗣

Events

• Admin Training @ GCC 2022: Online Training Day 🧑‍🏫

GitHub Activity

github Issues Reported

External Links

Favourite Topics

Favourite Formats