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Jan 17, 2025

Workshop series in 2025

Please help us circulate the workshop invitations to any relevant departments/groups, thanks!

Are you a student or academic, current or future user of the GenomeDK high-performance computing (HPC) system? Or are you just curious about HPC and how you can utilize it in your work? Do you need to learn to use GenomeDK, or wish to become a better and more organized user?

Then join us in this series of GenomeDK workshops where we guide you from a general introduction to advanced usage. Each workshop targets increasing difficulty levels, so you can join the sessions that fit you best.

Each workshop is scheduled for four hours, including a 45 min. lunch break.

There will be cake, coffee, and tea for attendants, so please remember to sign up.

Getting started with high-performance computing on GenomeDK

February 26, 2025, 10:00-14:00 @ 1253-317 (William Scharff)

Intended audience: For new or potential users of GenomeDK, or existing users with limited experience.

Topics:

  • Login and public-key authentication setup
  • File system organization
  • Basic Linux commands
  • Project management
  • Data transfer
  • Software management
  • The queueing system and your first batch jobs
  • Understanding and estimating resource usage

This workshop will be hosted by Samuele Soraggi (BiRC, MBG) and Dan Søndergaard (GenomeDK). There are 30 seats available.

Sign up here

Advanced use of GenomeDK

April 10, 2025, 10:00-14:00 @ 1253-317 (William Scharff)

Intended audience: For all users of GenomeDK, especially those already with some knowledge of the system.

Topics:

  • Multiple terminal sessions with tmux
  • Web applications and tunneling
  • Containerized software
  • Data synchronization with rsync
  • Pipelines and your first pipeline submission

This workshop will be hosted by Samuele Soraggi (BiRC, MBG) and Dan Søndergaard (GenomeDK). There are 30 seats available.

Sign up here

Pipelines on GenomeDK

June 4, 2025, 10:00-14:00 @ 1253-317 (William Scharff)

Intended audience: For users of GenomeDK who want to learn building complex and reproducible pipelines. Some of the content might be bioinformatics-specific.

Topics:

  • Why pipelines?
  • Main pipeline languages
  • Think through your pipeline architecture
  • Dependencies
  • Set software up and prepare your first pipeline
  • Submit!
  • Polish your resource requirements
  • Wrap up

This workshop will be hosted by Samuele Soraggi (BiRC, MBG) and Dan Søndergaard (GenomeDK). There are 30 seats available.

Sign up here