Martin Čech
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.
Tutorials
- Using Galaxy and Managing your Data / Understanding Galaxy history system 📝
- Using Galaxy and Managing your Data / JupyterLab in Galaxy 🧐
- Using Galaxy and Managing your Data / RStudio in Galaxy 🧐
- Galaxy Server administration / Deploying a compute cluster in OpenStack via Terraform 🧐
- Galaxy Server administration / Enable upload via FTP 🧐
- Galaxy Server administration / Galaxy Installation with Ansible 📝 🧐
- Galaxy Server administration / Galaxy Interactive Tools 🧐
- Galaxy Server administration / Reference Data with CVMFS 🧐
- Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
- Galaxy Server administration / Data Libraries 🧐
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
- Galaxy Server administration / Ansible 🧐
- Galaxy Server administration / Performant Uploads with TUS 🧐
- Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
- Galaxy Server administration / External Authentication 🧐
- Galaxy Server administration / Distributed Object Storage 🧐
- Galaxy Server administration / Managing Galaxy on Kubernetes 🧐
- Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
- Galaxy Server administration / Monitoring Galaxy and Pulsar with Sentry 🧐
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
- Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
- Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
- Galaxy Server administration / Automation with Jenkins 🧐
- Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
- Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
- Galaxy Server administration / Galaxy Installation on Kubernetes 🧐
- Galaxy Server administration / Upgrading Galaxy 🧐
- Galaxy Server administration / Galaxy Monitoring with Reports 🧐
- Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🧐
- Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
- Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
- Ecology / Species distribution modeling 🧐
- Climate / Visualize Climate data with Panoply netCDF viewer 🧐
- Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab 🧐
- Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
- Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) 🧐
- Statistics and machine learning / Text-mining with the SimText toolset 🧐
- Statistics and machine learning / Introduction to Machine Learning using R 🧐
- Contributing to the Galaxy Training Material / Including a new topic 🧐
- Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
- Contributing to the Galaxy Training Material / Running the GTN website locally using the command line 🧐
- Contributing to the Galaxy Training Material / Adding auto-generated video to your slides 🧐
- Foundations of Data Science / R basics in Galaxy 🧐
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R 🧐
- Transcriptomics / RNA Seq Counts to Viz in R 🧐
- Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease 🧐
- Development in Galaxy / Galaxy Webhooks ✍️ 🧐
- Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
Slides
- Galaxy Server administration / Terraform 🧐
- Galaxy Server administration / Controlling Galaxy with systemd or Supervisor 🧐
- Galaxy Server administration / uWSGI 🧐
- Galaxy Server administration / Galaxy Installation with Ansible 🧐
- Galaxy Server administration / Galaxy Monitoring 🧐
- Galaxy Server administration / Gearing towards production ✍️ 🧐
- Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐
- Galaxy Server administration / Galaxy Interactive Tools 🧐
- Galaxy Server administration / Reference Data with CVMFS 🧐
- Galaxy Server administration / Storage Management ✍️
- Galaxy Server administration / Galaxy on the Cloud 🧐
- Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
- Galaxy Server administration / Ansible 🧐
- Galaxy Server administration / Reference Genomes in Galaxy 🧐
- Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
- Galaxy Server administration / External Authentication ✍️ 🧐
- Galaxy Server administration / Empathy 🧐
- Galaxy Server administration / Advanced customisation of a Galaxy instance ✍️ 🧐
- Galaxy Server administration / Storage Management ✍️ 🧐
- Galaxy Server administration / Galactic Database ✍️ 🧐
- Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
- Galaxy Server administration / User, Role, Group, Quota, and Authentication managment 🧐
- Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
- Galaxy Server administration / Galaxy Troubleshooting ✍️ 🧐
- Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
- Galaxy Server administration / Server: Other 🧐
- Statistics and machine learning / Convolutional neural networks (CNN) Deep Learning - Part 3 🧐
- Contributing to the Galaxy Training Material / Creating Slides 🧐
- Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material 🧐
- Development in Galaxy / Scripting Galaxy using the API and BioBlend 🧐
- Development in Galaxy / Galaxy Interactive Tours 🧐
- Development in Galaxy / Galaxy Interactive Environments 🧐
- Development in Galaxy / Tool development and integration into Galaxy 🧐
- Development in Galaxy / Galaxy Webhooks ✍️ 🧐
- Development in Galaxy / Galaxy Code Architecture 🧐
- Introduction to Galaxy Analyses / A Short Introduction to Galaxy 🧐
- Introduction to Galaxy Analyses / Introduction to Galaxy 🧐
FAQs
Video Recordings
GitHub Activity
github Issues Reported
28 Merged Pull Requests
See all of the github Pull Requests and github Commits by Martin Čech.
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fix copypasta
devpaper-cut
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fix link to GTA video
assembly
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ML3 training: clarify what is the name of the input dataset
bugstatistics
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add more pers info to contributors
template-and-tools
- include webrick as a conditional dependency
Reviewed 61 PRs
We love our community reviewing each other's work!
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Youtube IDs are 11 characters only
template-and-tools
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link more things in admin via my.gat
admin
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FAQ for using data sources tools with Pulsar as default
admintemplate-and-tools
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Admin, mapping jobs with TPV: Fix a few speling mistakes
admin
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Update the admin troubleshooting slides
admin
News
GTN in Discourse
30 January 2024
Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure.
When you paste a GTN Frequently Asked Questions URL into the Galaxy Discourse, it will now be rendered directly in Discourse!
External Links
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