Learn from experts

Birte Kehr

Barcode correction for linked-read sequencing data

Florian Eggenhofer

Development of Architecture for Software Containers - practical computational reproducibility for everyone


Topics and who should attend


We address publicly used analysis infrastructures, bioinformatics service and research, as well as translational bioinformatics issues like integration of bio-banking, medical information (records) and the corresponding genomic information.

The topics discussed include, but are not limited to, ideas, new solutions and best practices in

  • high throughput data processing, data analysis and interpretation
  • reproducible research, workflow and tool management
  • benchmarking of data analysis workflows
  • data management, data sharing and data security
  • next-generation infrastructure, e.g. virtualization, cloud services, etc.

Furthermore we cover the evolving relationship between research groups and core facilities and foster exchange on core unit organization and management, e.g. in areas like service and project management, scientific cooperation, bioinformatics teaching and bioinformatics career opportunities in core units.


Everyone working in a bioinformatics core unit or tasked with state-of-the art bioinformatics data analysis should not miss this event.


ÄBC2'18 is organized by

  • Dieter Beule (BIH Berlin)
  • Szymon Kielbasa (Leiden University Medical Center)
  • Sven Nahnsen (University of Tübingen)
  • Sven Rahmann (University Hospital Essen, University of Duisburg-Essen, UA Ruhr)
  • Daniel Stekhoven (ETH Zürich, Swiss Institute of Bioinformatics (SIB))

Call for Contributions

Share your experiences!

Contributed Talks

We are inviting the submission of talks on all aspects of bioinformatics core units, including scientific data analysis, data integration, administrative issues and much more.

For 2018, we are suggesting a number of focus topics that we believe to be of particular interest to the community:

  • implications of new data protection law (DSGVO)
  • k-mer methods in production pipelines
  • cloud computing in the hospital
  • follow-up to last year’s ring trial: RNA-seq best practices

Please note that this list is not exclusive, and you can still propose talks on any other topic relevant to core units!

To contribute, please prepare a short or extended abstract of your talk (1--3 pages) with your name(s), affiliation(s) and a summary of the points to be discussed. If there are more submissions than talk slots, the organizing committee will select talks based on perceived general interest and to balance different topics.

We are not looking for polished research papers, but for good and helpful ideas gained from practical experience and daily work.

There will be no published proceedings, although we may discuss at the workshop if we should send collected abstracts to a PrePrint server.

Practical Session and Breakout Groups

In the afternoon, we plan a practical session:

  • Bring, show, discuss, ask questions about your own workflow.

Please share your workflow with your peers and let them comment on it and gather feedback. We anticipate that we will be able to discuss a number of different workflows in small groups.

We will also have breakout groups to discuss topics of current interest Topics of discussion may include, but are not limited to:

  • methylome analysis
  • whole genome sequencing: explain every read
  • storage conundrum

Where to send contributions

Please send your contributions by email as a PDF attachment to until September 10, 2018.


When, what and who?

When What Who/Where
09:30 Arrival, registration, coffee on site
10:20 Welcome address the organizers
10:30 Session 1 (Keynotes and discussion)
10:30 Development of architecture for software containers - practical computational reproducibility for everyone Florian Eggenhofer (Freiburg)
11:10 Barcode correction for linked-read sequencing data Birte Kehr (BIH, Berlin)
11:45 Discussion: Are k-mer methods ready for production use? Sven Rahmann (Essen)
12:20 Case study: Data management @QBIC Sven Nahnsen (Tübingen)
13:00 Lunch break on site
14:00 Session 2 (Contributed talks): Practical workflows and data management
14:00 Case study: Data management @CUBI Dieter Beule (BIH, Berlin)
14:15 Containerized microservices on a Kubernetes cluster for browsing shared biomedical data Michael Huttner (Regensburg)
14:35 The core facility "Computational Bioanalytics" at the Center for Medical Research Andrea Groselj-Strele, Slave Trajanoski (Med U Graz)
14:50 Update on last year's RNA-seq ring trial Dieter Beule (BIH, Berlin)
15:10 Coffee break on site
15:40 Session 3: Parallel break-out groups Moderator
1. Methylome analysis workflows Sven Rahmann
2. Whole genome analysis: every read explained? Sven Nahnsen
3. The storage conundrum Dieter Beule
17:00 Presentation and discussion of BOG 1 results
17:20 Presentation and discussion of BOG 2 results
17:40 Presentation and discussion of BOG 3 results
18:00 End of workshop

This schedule (updated: 25.09.2018) is final. Times are approximate.

Travel and Venue

How to find it

The workshop is part of the workshops of the German Conference on Bioinformatics (GCB) 2018 in Vienna.

The precise room for the workshop will be assigned and announced shortly before the meeting, depending on the number of participants.

Please see the venue information on the GCB website for more information.


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