Kubernetes for Computational Biology (UKE internal training)

Date: 11th July 2025, Time: 11:00-12:00

Location: Seminar room 1.XY (Hybrid-session via Zoom), Zentrum für Molekulare Neurobiologie Hamburg (ZMNH), Building S50, UKE

Instructor: Sven Heins, Institute of Medical Systems Bioinformatics, UKE

Language: English

Prerequisites:

• UKE employee
• Basic command-line/terminal experience
• Familiarity with Docker containers (preferred but not required)
• Basic knowledge about at least one of the tools: Jupyter notebooks, VSCode or Nextflow

Description: This hands-on workshop is designed for UKE bioinformaticians, computational biologists, and biomedical researchers who want to use Kubernetes for scalable scientific computing. Whether you’re running CPU-intensive genomics pipelines, interactive data analysis notebooks, or GPU-accelerated machine learning models, this workshop will teach you how to deploy and manage your computational workloads on our Kubernetes cluster.

We’ll cover both theoretical concepts and practical implementation, with ready-to-use templates for common use cases. Participants should have basic command-line experience and familiarity with containerization concepts (Docker).

Topics:

• Kubernetes fundamentals and architecture for scientific computing (~15 minutes)
• Live demo of common use cases (~15 minutes)
• Practical session (~30 minutes)
  • Deploying interactive Jupyter notebooks
  • Running scalable bioinformatics pipelines using Nextflow on Kubernetes
  • GPU-based deep learning workflows in VSCode

Registration for this training is open.