Workshops
will take place on Monday, 22 September 2025
Overview:
Detailed Workshop Programme:
WS1) Bioinformatics education
Organizers: Jan Grau (MLU Halle); Stefan Kurtz (Universität Hamburg); Kay Nieselt (Eberhard Karls Universität Tübingen); Sven Rahmann (Universität des Saarlandes, Saarbrücken); Ralf Zimmer (Ludwig-Maximilians-Universität München)
Participants: max. 30
- Which essential topics and skills should be covered by a B.Sc. in bioinformatics with regard to
- Mathematics
- Computer Science, incl. theory and application of Machine Learning / Artificial Intelligence
- Life Sciences
- Core Bioinformatics
- How should ECTS/CPs be distributed among these topics? What proportion of core bioinformatics modules should be reached?
- What is a reasonable balance between theoretical and practical (wet lab, programming, etc.) courses?
- Which proportion of ECTS/CPs should be held flexible to
- allow for setting a university-specific focus/specialization or
- allow students to follow their topics of interest?
- What language requirement should be stated, should the B.Sc. be taught (entirely) in English?
WS2) simpleVM [deNBi]
Organizers: Peter Belmann & Alexander Sczyrba (FZ Jülich / deNBI)
- Cloud Computing Basics
- Managing Instances
- Managing Volumes
- Using Research Environments for Analyzing Results
- Scaling with a SimpleVM Cluster
- Handling Data in Object Storage
WS3) From a Collection of Scripts to a Pipeline
Organizers: Mark Polster, Famke Bäuerle & Sven Nahnsen (University of Tuebingen)
- nextflow principles
- nf-core and its relationship to nextflow
- exploration of an example pipeline
- hands-on creation of a pipeline
- using the nf-core template
- exploration of available modules
- writing new modules
WS4) Datavzrd
Organizers: Felix Wiegand & Johannes Köster (Universität Duisburg-Essen)
- Brief introduction to Datavzrd
- Highlight of its core strengths in generating portable, visually rich, and interactive reports
- Hands-on tutorial on how to use the tool effectively
WS5) Mastering GHGA: From Metadata Preparation to Secure Data Access
Organizer: Vanessa González Ribao (German Human Genome-Phenome Archive / DKFZ)
- Understanding Genome Archives and FAIR Principles
- Metadata & Data Preparation for Submission
- Efficiently Browsing & Searching the GHGA Data Portal
- Best-Practice Data Access & Legal Considerations
- Interactive Q&A and Hands-On Experience
WS6) Computational Pangenomics [deNBI]
Organizers: Tizian Schulz & Jens Stoye (Universität Bielefeld / deNBI)
- Introduction to computational pangenomics
- Investigating a pangenome's diversity with panacus and hands-on
- Pangenomic core detection with Corer and hands-on
- Querying a graphical pangenome with PLAST and hands-on
- Phylogenomic reconstruction with SANS and hands-on
WS7) Automated metabolic modelling: Building, analysing and simulating genome-scale metabolic models in Python
Organizers: Carolin Brune & Andreas Dräger (Martin Luther University Halle-Wittenberg)
- Basic understanding of constraint-based metabolic models and their application(s)
- Learning the basic steps of how genome-scale metabolic models are generated and further curated
- Getting insights into how these models can be utilised
- Hands-on experience on how to use the toolbox refineGEMs
- Experience in model reconstruction using different workflows from SPECIMEN
WS8) Spatial domain identification: computational methods for discovering tissue architecture
Organizers: Robin Khatri (University Medical Center Hamburg-Eppendorf)
- Identify spatial domains in single-cell spatial transcriptomics data
- Use unsupervised methods for detection and interpretation
- Analyze tissue dynamics in health and disease
- Apply domain identification algorithms hands-on
