Learn from experts

Camille Stephan-Otto Attolini

Prof. Camille Stephan-Otto Attolini is the core facility manager of the Bioinformatics / Biostatistics Unit at the Institute for Research in Biomedicine (IRB) in Barcelona. Some while ago her unit started billing users for their services. In a lessons-learned session we will hear about her experiences.

Nicola Aceto

Prof. Nicola Aceto is the group leader of the Cancer Metastasis lab at the University of Basel. His research focuses on the analysis of human circulating tumor cells, aiming towards the identification of key vulnerabilities of the metastatic process in cancer patients.

Johannes Köster

Dr. Johannes Köster received his doctoral degree from TU Dortmund, Germany, and held postdoctoral positions at Harvard and CWI Amsterdam before moving to a group leader position at the University of Duisburg-Essen in 2017. He is well known for his work on Snakemake and the bioconda project.


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‘17 is organized by

  • Dieter Beule (BIH Berlin)
  • Sven Nahnsen (University of Tübingen, local)
  • 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!

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.

In addition, in 2017, we have a focus session on RNA-seq analysis. If you have experiences with RNA-seq to share, please indicate that you want to be considered for the focus session.

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.

Please send your contributions by email as a PDF attachment to until August 30, 2017.


When, what and who?

When What Who/Where
09:30 Arrival, registration, coffee on site
10:20 Welcome address
10:30 Session 1: Core Facility Management
10:30 Workflow and Tool Management Johannes Köster
11:20 Bioinformatics and Biostatistics as Full Service in Biomedical Research Camille Stephan-Otto
12:10 Lunch break (finger food, drinks, coffee) on site
13:30 Session 2: Contributed Topics
13:30 Varcatch: a method to reduce alignment reference bias Szymon M. Kielbasa, Leiden University Medical Center
13:50 Making bioinformatics tools accessible to non-computer scientists Marcel Bargull, TU Dortmund
14:10 Reproducible data analysis for the people with the SUSHI framework Hubert Rehrauer, FGCZ
14:30 Lessons learnt on building reproducible NGS pipelines Hailang (Leon) Mei, Leiden University Medical Center
14:50 Discussion
15:00 Coffee break (cake, fruits, drinks, coffee) on site
15:30 Session 3: Focus on RNA-seq
15:30 Single cell-resolution parallel exome and transcriptome analysis of human circulating tumor cells Nicola Aceto
16:10 Introduction to RNA-seq break-out session
16:15 Discussion in break-out groups (BOGs)
BOG 1: Visualization of differential expression analysis results Coordinator: D. Stekhoven
BOG 2: RNA-seq benchmark challenge Coordinator: S. Nahnsen, S. Rahmann
BOG 3: Interactive reporting of RNA-seq results Coordinator: H. Rehrauer (FGCZ)
17:15 Presentation and discussion of BOG 1 results
17:35 Presentation and discussion of BOG 2 results
17:55 Presentation and discussion of BOG 3 results
18:15 Conclusion and joint imbiss / beer

The is the final schedule (18.09.2017).


Join us!

Please register as early as possible to facilitate our planning and to enjoy a substantial discount on the registration fee.

Registration includes full participation, coffee and food.

Category Early (-Jul 31) Regular (Aug 1 - Aug 31)
Student 90 EUR 120 EUR
Academic 150 EUR 170 EUR
Industry 300 EUR 400 EUR

Please register using the registration form.

Travel and Venue

How to find it

The workshop is co-located with the workshops of the German Conference on Bioinformatics (GCB) 2017 in Tübingen.

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

Please visit the GCB website for general information about travel and accomodation in Tübingen in September.


Imprint and Disclaimer

In case of questions or comments about the website, please contact us.

Imprint is the website of the Annual European Bioinformatics Core Community Workshop (ÄBC2). The website is published by the organizers, namely Dieter Beule (BIH Berlin), Sven Nahnsen (Tübingen), Sven Rahmann (University of Duisburg-Essen), Daniel Stekhoven (ETH Zürich).


Although the organizers take all possible care to ensure the correctness of published information, no warranty can be accepted regarding the correctness, accuracy, uptodateness, reliability and completeness of the content of this information.

The organizers expressly reserve the right to change, to delete or temporarily not to publish the contents wholly or partly at any time and without giving notice.

Liability claims against the organizers or their affiliated institutions, namely BIH Berlin, University of Tübingen, University of Duisburg-Essen, ETH Zürich, because of tangible or intangible damage arising from accessing, using or not using the published information, through misuse of the connection or as a result of technical breakdowns are excluded.

The organizers have not checked third party web sites, i.e. web sites not located on their servers or in their area of influence, that may be connected to this web site via links, and do not accept any responsibility for the contents or the services offered thereon.