Crash-Course: 'HPC in Biomedical Research'

We are happy to announce a short, crash-course version of “HPC in Biomedical Research”. Note that this course is a directly after the HPC User Meeting on October 26, 2023.

Date and Location

October 26th, 2023, 11:30-16:00 (on-site, Charité Campus Mitte, CCCC, Invalidenstr. 80, Seminar Room in Level 3 Hörsaal Pathologie, Virchowweg 15)

  • coffee and lunch break included

You can find the slides here:

The polls & quizzes will be available here:

Scope and Aim

High-Performance Computing (HPC) is a widely applicable technique that has many applications in the processing of large data volumes as created by high-throughput assays in the life sciences. This short course provide a hands-on introduction in how to use the BIH HPC system.

In particular, participants will

  • get an overview of HPC
  • get an introduction of job submission, management, and troubleshooting with Slurm
  • get an outlook at further topics such as workflow managers, maintaining software installations, etc.

The workshop consists of 5*45min (5 Unterrichtseinheiten) with explanation of the topics above, hands-on tasks, and short quizzes to test the “Lernerfolg”.

Time Event Topic
10:00-11:00 User Meeting see here
11:00-11:30 Both Coffe Break
11:30-13:00 Crash Course Part 1
13:00-13:45 Crash Course Lunch Break (with finger food)
11:45-16:00 Crash Course Part 2
Requirements for Participations

Participants must:

  • have basic knowledge of the Linux operating system and programming experience in the Python programming language;
  • work with a group leader with Charité, BIH, or MDC affiliation;
  • obtain an account on the BIH HPC (e.g., to hpc-login-1) - their group leader/PI can register this for free via email to

As we could acquire a larger room this time, we can accomodate for 30 participants. Registration is quired. Be sure to register early on to reserver your spot! Preference will be given to PhD students.


Registration is required. Please register using the following link by October 12 (the earlier the better)

We assume that all participants who visit for the HPC course will also visit the cluster user meeting.

Please send the self-assessment from below with your registration email to

We are looking forward to your participation!

Self-Assessment Form
  1. My favourite programming language is ________
  2. On a level from 1-10, I am on level in the programming language from (1) _______
  3. The last thing I learned (in the programming language from (1) to get to my level was): _______
  4. During my daily HPC usage, I’m struggling most with the following 3 points: _______
  5. My expectation is that I will learn the following concrete two points: _______
Change Of Location

Because of the high number of registrations, we had to change the location to a larger room. The new location is:

  • Hörsaal Pathologie
  • Virchowweg 15

Please read the following notes:

  • The chairs in the auditorium are not very comfortable; consider bringing a seat cushion.
  • We have a large number of registrations but we will still try to keep the course interactive. Bring your laptop, ensure that you have access to WiFi, and via Charite/MDC VPN to the HPC system (and you have a login on the system itself).
  • There will be a coffee break and cold/finger food lunch break. We regret that we cannot cater to all dietary restrictions, so please plan accordingly.
  • While we have some catering, consider bringing a water bottle as the facilities in the building are limited.

We will try to answer your questions sent to

Last modified: Oct 26, 2023