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Annual European Bioinformatics Core Community (AEBC2) Workshop 2020


Thursday, 3rd September


13:30 to 16:30 (CEST)


  • Dieter Beule | Berlin Institute of Health, Germany
  • Sven Rahmann | University of Duisburg-Essen, Germany
  • Sven Nahnsen | University of Tübingen, Germany
  • Daniel J. Stekhoven | ETH Zurich, Switzerland
  • Camille Stephan Otto Attolini | IRB Barcelona, Spain
  • Chris Evelo | Maastricht University, Netherlands


  • Mitchell P. Levesque | University Hospital Zurich, Switzerland
  • Sarah Hunt | EMBL-EBI, United Kingdom
  • Peter Krawitz | University of Bonn, Germany


The number of bioinformatics core units in industrial and academic research environments is growing rapidly. The AEBC2 workshop provides an exchange opportunity for scientific and service aspects of bioinformatics core facilities in Europe.

Furthermore, there is an increasing need for bioinformatics translated to clinical application as a service. Examples include omics-informed precision oncology, rare genetic diseases, infectious diseases, or gene therapy. Due to the field fast evolving, there is much uncertainty about best practices, tool stability, and much re-invention and duplication is happening. This workshop aims to bring together leading researchers and practitioners in these areas to exchange latest approaches, experiences, benchmark results, protocols and best practice guidelines for reporting evidence to clinicians. The workshop format will include invited and contributed talks selected from an open call for contributions, structured discussions in break-out groups and the plenum. See also Format below.

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, data security, and legal aspects
  • 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.

The goals of the workshop are:

  • fostering a community of bioinformaticians working in providing clinical services, including researchers and companies producing tools for or services to them
  • understanding the strengths and weaknesses of available technologies
  • exchanging results of benchmark studies, of systematic data and tool quality assessment efforts
  • converging on study designs for data and tool quality assessment efforts
  • learning about best practices: what to do and what to avoid in bioinformatics when offered as a service, especially to clinician
  • developing best practices of reporting evidence to clinicians.

Target audience

Everyone working in a bioinformatics core unit or tasked with state-of-the art bioinformatics data analysis should not miss this event. This installment will feature several projects translating state-of-the-art data science into clinical application and the role core facilities can play in such endeavors. We expect 40-70 participants.


Time (CEST)
13:30 - 14:30 Part 1 - The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support - Mitchell P. Levesque
14:30 - 15:30 Part 2 - Interpreting Genetic Variation in Rare Disease Research with the Ensembl Variant Effect Predictor - Sarah Hunt
15:30-16:30 Part 3 - Next-generation phenotyping with deep convolutional neural networks on medical imaging data (portraits, x-rays, funduscopies) - Peter Krawitz