More than 120 participants joined us for the first Galaxy User Conference in Freiburg. 
It started with a tribute from Björn to Stephen Hawkings.
Followed by several talks across diverse topics:
- “de.NBI & RBC” by Andreas Tauch (Bielefeld, DE) and Rolf Backofen (Freiburg, DE)
- “Galaxy HiCExplorer” by Joachim Wolff (Freiburg, DE)
- “Analysis of the cardiac myocyte epigenome using Galaxy” by Ralf Gilsbach (Freiburg, DE)
- “Using direct reprogramming to find the master regulators of renal tubulogenesis and factors leading to congenital kidney defects” by Sören Lienkamp (Freiburg, DE)
- “Galaxy tools and workflows for metabolomics: A community effort to make data processing and analysis accessible, reproducible, and transparent” by Ralf Weber (Birmingham, UK)
- “Workflow4Metabolomics - Towards an international computing infrastructure and a tools showcase for Metabolomics” by Christophe Caron (Rennes, FR)
- “Deployment of genome databases for insects using Galaxy Genome Annotation” by Anthony Bretaudeau (Rennes, FR)
- “Galaxy-E: A french initiative dedicated to Macro-Ecological data analysis” by Yvan Le Bras (Paris, FR)
- “The ELIXIR Communities launch” by John Hancock (ELIXIR, UK) and Frederik Coppens (Gent, BE)
At the end of the first day, Simon Gladman (from Australia) and Björn officially launched the!
After a nice dinner at Martin’s Bräu, the second (and last) day started. We had 13 talks, ranging from Beer and Proteomics to Imaging:
- “The Beerome – Science for the Mind and the Stomach” by Teresa Müller (Freiburg, DE)
- “Gene discovery with KnetMiner” by Ajit Singh (Hertfordshire, UK)
- “Fruit Fly reproduction” by Ihor Yurkevych (Ivano-Frankivsk, UA)
- “Proteomic analyses of mass spectrometry data using OpenMS in Galaxy” by Matthias Fahrner (Freiburg, DE)
- “Quality control and analysis of large scale MALDI imaging data of peptides from formalin-fixed paraffin-embedded tissues within the Galaxy environment” by Melanie Föll (Freiburg, DE)
- “Galaxy for microscopy image analysis workflows and systematic phenotyping” by Thomas Wollmann (Heidelberg, DE)
- “RNA Workbench” by F. Eggenhofer – Freiburg, DE
- “Integrated analysis of miRNA-mRNA regulatory networks in chordoma tumors using Galaxy” by Beata Scholz (Debrecen, HU)
- “Extracting biological sense from RNA-seq time series in dynamic biological systems” by Daria Onichtchouk (Freiburg, DE)
- “Microbiota analysis using Galaxy” by Saskia Hiltemann (Rotterdam, NE)
- “Galaxy Australia/USA communities” by Simon Gladman (Melbourne, AU) and Anton Nekrutenko (PSU, USA)
- “The Galaxy Training Network” by Bérénice Batut (Freiburg, DE)
We are discussing with the different speakers and we hope to add links to the slides soon. We will keep in touch!
Thanks a lot to all the speakers and participant! See you all in Freiburg in 2019 for GCC!
25968925417 f9d0b33f50 o

Frank Oliver Glöckner, Michael Diepenbroek, Dietmar Schomburg, Jörg Overmann, Antje Chang, Ida Schomburg, Lisa Jeske, Sandra Placzek, Janine Felden, Ivaylo Kostadinov, Lorenz Reimer, Uwe Schindler, (BioData) Daniel Arend, Uwe Scholz (GCBN) Wolfgang Müller (de.NBI-SysBio)

03-09-2018 to 07-09-2018, 9:00-18:00

Braunschweig Integrated Centre of Systems Biology (BRICS)
Rebenring 56
D-38106 Braunschweig

Research Data Management has been recognised as a central part of “Good Scientific Practice” already many years ago. In 2007 the OECD (Organisation for Economic Co-operation and Development) published recommendations that data from publicly funded research has to become publicly available. This was followed by a series of publications on the international and national level that emphasise the value of data sharing and publication for innovation and economy. The ability to compare and integrate research data will not only fuel individual research projects but is a cornerstone to address broad questions in health and disease management and global change.
The vision that we want to promote in the summer school is that 1) any scientist has easy access to research data, 2) scientists can share data across borders, 3) structures for long-term archiving are established, 4) infrastructures for data acquisition and management are available including specialists that support researchers with all aspects of the Data Life Cycle and 5) publishing of research data promotes the scientific reputation and career path.

Learning goals:
The goal of this de.NBI summer school is to raise awareness for the importance of proper research data management in general but will also provide a practical toolbox for the acquisition, curation, documentation, archiving and publication of research data following the FAIR (Findable, Accessible, Interoperable and Re-usable) data principles. Furthermore, a practical training on accessing the data for re-use and integration are part of the learning goals.

The training course is targeted towards early career scientists like PhD students and Postdocs who want to share, archive and publish their research data.
No programming skills are necessary.
Basic knowledge about research data management would be a plus.

Research Data Management, Data Management Plan, Data Life Cycle, Ontologies, Standards, Data curation, Data archiving and publication, Data licensing, CBD, Nagoya protocol


Frank Oliver Glöckner
This email address is being protected from spambots. You need JavaScript enabled to view it.

More Information:

The de.NBI cloud is a fully academic cloud infrastructure, free of charge for academic users, where currently five cloud centers provide compute and storage resources.

During 2017, de.NBI was integrated into ELIXIR AAI which acts as a backbone for the connection of the five compute centers and allows users to manage cloud projects and access the cloud infrastructure using the authentication service of their home institutions.

In this webinar (Wed 7 March 2018, 14:00 CET), Peter Belmann (de.NBI cloud governance) presented how de.NBI made use of ELIXIR AAI and demonstrated how a potential user logs in to the portal, applies for and manages his project, and finally starts using the assigned resources in the cloud.

Michal Prochazka of ELIXIR-CZ complemented Peter’s presentation by describing how the integration was done on the ELIXIR AAI side.


The 12th CeBiTec Symposium scheduled for March 19 to 21, 2018, will focus on big data in medicine and biotechnology. It is organized as a joint conference of the CeBiTec,the German Network for Bioinformatics Infrastructure (de.NBI), and the Bielefeld Center for Data Science (BiCDaS). The CeBiTec is responsible for organizing the basic sessions of the big data symposium. The de.NBI network will organize the second day which is focused on the presentation of 12 use cases which are currently discussed in the ELIXIR organization. BiCDaS finally contributes to the round table discussion at the end of the conference which will deal with ethical and legal aspects of big data in medicine and biotechnology. The title of the symposium is well chosen since the CeBiTec is deeply involved in the production and the analysis of big data sets. On the other hand, the actual plan to establish a Faculty of Medicine at Bielefeld University underlines the goal of the symposium to discuss medical data

The 12th CeBiTec Symposium will follow a well established programme structure. At the end of the first day, a session with short contributions of young scientists is planned, followed by a poster session. Concerning the second day, the detailed presentation of ELIXIR use cases will be followed by two Distinguished Symposium Lectures informing on ethical and legal considerations of medical data. At the end of the second day the symposium dinner in a nearby restaurant is on the agenda. The third day of the symposium, finally, is reserved for presentations on the role of big data in
biotechnology, but also on the role of cloud computing in the age of big data science. The organizers of the 12th CeBiTec Symposium look forward very much to interest many scientists from Bielefeld University, from the de.NBI network, but also from abroad.