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.

• Topic: Galaxy Server administration

Tutorials

• Development in Galaxy / Setting up a dev Onedata instance 🧐
• Development in Galaxy / Galaxy Webhooks ✍️ 🧐
• Development in Galaxy / JavaScript plugins 🧐
• Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
• 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 / Preview the GTN website as you edit your training material 🧐
• Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours 🧐
• Contributing to the Galaxy Training Material / Adding auto-generated video to your slides 🧐
• Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
• Teaching and Hosting Galaxy training / Running a workshop as instructor 🧐
• Statistics and machine learning / Machine learning: classification and regression 🧐
• Statistics and machine learning / Regression in Machine Learning 🧐
• Statistics and machine learning / Text-mining with the SimText toolset 🧐
• Statistics and machine learning / Basics of machine learning 🧐
• Statistics and machine learning / Introduction to Machine Learning using R 🧐
• Statistics and machine learning / Fine tune large protein model (ProtTrans) using HuggingFace 🧐
• Statistics and machine learning / Classification in Machine Learning 🧐
• Statistics and machine learning / Age prediction using machine learning 🧐
• Statistics and machine learning / Deep Learning (Part 3) - Convolutional neural networks (CNN) 🧐
• Statistics and machine learning / Introduction to deep learning 🧐
• Statistics and machine learning / A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy 🧐
• Statistics and machine learning / Clustering in Machine Learning 🧐
• Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 🧐
• Epigenetics / Identification of the binding sites of the Estrogen receptor 🧐
• Epigenetics / Formation of the Super-Structures on the Inactive X 🧐
• Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🧐
• Computational chemistry / High Throughput Molecular Dynamics and Analysis 🧐
• Climate / Visualize Climate data with Panoply netCDF viewer 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab 🧐
• Single Cell / Inferring single cell trajectories with Scanpy (Python) 🧐
• Single Cell / Pre-processing of Single-Cell RNA Data 🧐
• Single Cell / Filter, plot and explore single-cell RNA-seq data with Scanpy 🧐
• Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 🧐
• Single Cell / Single-cell ATAC-seq standard processing with SnapATAC2 🧐
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R 🧐
• Transcriptomics / RNA Seq Counts to Viz in R 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis 🧐
• Using Galaxy and Managing your Data / Importing (uploading) data from Onedata 🧐
• Using Galaxy and Managing your Data / JupyterLab in Galaxy 🧐
• Using Galaxy and Managing your Data / Creating high resolution images of Galaxy Workflows 🧐
• Using Galaxy and Managing your Data / RStudio in Galaxy 🧐
• Using Galaxy and Managing your Data / Automating Galaxy workflows using the command line 🧐
• Using Galaxy and Managing your Data / Exporting to Onedata remote 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 📝 🧐
• Using Galaxy and Managing your Data / Getting started with Onedata distributed storage 🧐
• Using Galaxy and Managing your Data / Onedata user-owned storage 🧐
• Proteomics / Mass spectrometry imaging: Loading and exploring MSI data 🧐
• Proteomics / Protein FASTA Database Handling 🧐
• Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS 🧐
• Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) 🧐
• Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
• Proteomics / Peptide and Protein ID using OpenMS tools 🧐
• Proteomics / Secretome Prediction 🧐
• Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
• Galaxy Server administration / Enable upload via FTP 🧐
• Galaxy Server administration / Reference Data with CVMFS 🧐
• Galaxy Server administration / Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD) 🧐
• 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 / Setting up Celery Workers for Galaxy 🧐
• Galaxy Server administration / Customizing the look of Galaxy (Manual) 🧐
• 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 / Deploying a compute cluster in OpenStack via Terraform 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐
• Galaxy Server administration / Distributed Object Storage 🧐
• Galaxy Server administration / Monitoring Galaxy and Pulsar with Sentry 🧐
• Galaxy Server administration / Managing Galaxy on Kubernetes 🧐
• Galaxy Server administration / Customizing the look of Galaxy 🧐
• 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 🧐
• Galaxy Server administration / Galaxy Installation on Kubernetes 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
• Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease 🧐
• FAIR Data, Workflows, and Research / RO-Crate in Python 🧐
• FAIR Data, Workflows, and Research / RO-Crate - Introduction 🧐
• FAIR Data, Workflows, and Research / Best practices for workflows in GitHub repositories 🧐
• Ecology / Species distribution modeling 🧐
• Foundations of Data Science / R basics in Galaxy 🧐

Slides

• Development in Galaxy / Galaxy Code Architecture 🧐
• Development in Galaxy / Galaxy Webhooks ✍️ 🧐
• Development in Galaxy / Tool development and integration into Galaxy 🧐
• Development in Galaxy / Galaxy Interactive Tours 🧐
• Development in Galaxy / Scripting Galaxy using the API and BioBlend 🧐
• Development in Galaxy / Galaxy Interactive Environments 🧐
• Contributing to the Galaxy Training Material / Creating Slides 🧐
• Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material 🧐
• Statistics and machine learning / Regression in Machine Learning 🧐
• Statistics and machine learning / Introduction to Machine learning 🧐
• Statistics and machine learning / Fine-tuning Protein Language Model 🧐
• Statistics and machine learning / Classification in Machine Learning 🧐
• Statistics and machine learning / Convolutional neural networks (CNN) Deep Learning - Part 3 🧐
• Transcriptomics / Introduction to Transcriptomics 🧐
• Galaxy Server administration / Empathy 🧐
• Galaxy Server administration / Galaxy Monitoring 🧐
• Galaxy Server administration / User, Role, Group, Quota, and Authentication managment 🧐
• 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 / Storage Management ✍️
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Controlling Galaxy with systemd or Supervisor 🧐
• Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐
• Galaxy Server administration / Terraform 🧐
• 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 / Gearing towards production ✍️ 🧐
• 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 🧐
• Introduction to Galaxy Analyses / A Short Introduction to Galaxy 🧐
• Introduction to Galaxy Analyses / Introduction to Galaxy 🧐

FAQs

• Renaming a collection

Video Recordings

• Galaxy Server administration / Ansible 💬
• Galaxy Server administration / Ansible 💬 🗣

GitHub Activity

github Issues Reported

29 Merged Pull Requests

See all of the github Pull Requests and github Commits by Martin Čech.

• fix reports nginx config to avoid localhost issues
  admin
• fix copypasta
  dev
  paper-cut
• fix link to GTA video
  assembly
• ML3 training: clarify what is the name of the input dataset
  bug
  statistics
• add more pers info to contributors
  template-and-tools

Reviewed 62 PRs

We love our community reviewing each other's work!

• Add esg metadata for partners and content
  admin
  dev
  variant-analysis
  transcriptomics
  template-and-tools
• Youtube IDs are 11 characters only
  template-and-tools
• link more things in admin via my.gat
  admin
• FAQ for using data sources tools with Pulsar as default
  admin
  template-and-tools
• Admin, mapping jobs with TPV: Fix a few speling mistakes
  admin

News

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