Annual European Bioinformatics Core Community (AEBC2) Workshop 2022

Workshop details
  • Date: Sunday, September 18th
  • Time: 09:00 to 13:00 CEST
  • Format: Face-to-face
  • Camille Stephan-Otto Attolini, IRB Barcelona (Spain)
  • Dieter Beule, Berlin Institute of Health (Germany)
  • Sven Rahmann, Saarland University (Germany)
  • Sven Nahnsen, Universität Tübingen (Germany)
  • Daniel J. Stekhoven, ETH Zurich (Germany)

The AEBC 2 workshop has been established as a yearly meeting of European bioinformatics core facilities, covering all scientific and service aspects. Each year, there is a different focus topic; for 2022 we selected “Mass Spectrometry and Multi-Omics Bioinformatics”


The number of bioinformatics core units in industrial and academic research environments is growing rapidly. The AEBC 2 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’s 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 services 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 clinicians
  • 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 instalment will feature several projects translating state-of-the-art data science into clinical application and the role core facilities can play in such endeavours.

Invited speakers

Phillip Mertins, BIMSB/MDC Berlin, Germany
Marina Gay, BIST/IRB Barcelona

09:00 – 09:15Welcome Address
Session I
09:15– 10:00Keynote presentation & discussion
Phillipp Mertins, BIMSB/MDC Berlin, Germany
Title: TBC
10:00 – 10:20Bioinformatics core facility management training – availability and challenges
Eva Alloza, Barcelona Supercomputing Center (BSC)
Sven Nahnsen, University of Tübingen
10:4011:00 Cell type-specific gene co-expression modules and expression signatures define tumor heterogeneity in melanoma patients
Lars Bosshard, ETH Zurich
Session II
11:15-12:00Keynote presentation & discussion
Marina Gay, BIST/IRB Barcelona, Spain
Title: “Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN”
12:0012:45Best Practice Session (Open Discussion & One Slide Presentations)
12:4513:00Closing Remarks
Social Event

In addition we will organise a social event in the evening for all participants to further foster core unit networking. Please do sent an email to info@aebc2.eu by 1st of September 2022 if you want to participate.