New Course: 'HPC in Biomedical Research'

We are happy to announce the course “HPC in Biomedical Research”.

Date and Location

August 28th - September 1st, 2023, 08:00 – 15:30 (on-site, Charité Campus Mitte)

Scope and Aim

This lab course provides an introduction to the use of High-Performance Computing (HPC) in biomedical research. In particular, participants will

  • get an overview of HPC and its role in biomedical research
  • obtain a solid understanding of the Slurm job scheduler for job submission, obtaining job/cluster state, and debugging issues with jobs
  • learn about applying Python for scientific programing in the life sciences for numerical and machine learning
  • using the Snakemake workflow management system for reproducible and scalable data anlysis on HPC systems

The course consists of a 90 min seminar in the morning followed by an “Praktikum” where participants can apply their learnings in the context of their PhD projects. Participant will discuss their learnings at the end of each day and give a short (5min) presentation at the end of the week.

Requirements for Participations

Participants must:

  • be enrolled as PhD students in one of the programs of Promotionsumgebung Charité;
  • 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

Registration is required. Please reserve your spot via email to by August 20 (the earlier the better). Please enclose a short description of your PhD project and a summary of your Linux/Python experience.

We are looking forward to your participation!

Last modified: Jul 28, 2023