ELIXIR: an international brew for smarter big data management and beyond

21 June 2017

​In our labs and beyond, massive and ever-increasing amounts of data are being generated. We have our own VIB Bioinformatics Core to help us tackle complex analyses, but the hyper-fast evolution of big data has pushed life science professionals to look at the issue – and possible solutions – on a larger scale. That’s where the European initiative ELIXIR comes in, boasting an ambitious goal: making the life of biologists and bioinformaticians easier.

Across the world, we’re all in it together – and we’re all experiencing firsthand that data management is anything but a walk in the park. As a result, the 2014 creation of a data infrastructure at the supranational level was a logical next step. Pooling together resources from across Europe – including databases, software tools, training materials, cloud storage and supercomputers – ELIXIR was launched as an intergovernmental organization. It has grown to 21 member states, currently the largest initiative of the European Strategy Forum on Research Infrastructures (ESFRI).

Housekeeping vs. The real deal
Headquartered in the UK, ELIXIR is comprised of ‘nodes’, or networks of organizations located within each member state. Here in Belgium, our VIB-UGent Center for Plant Systems Biology is coordinating ELIXIR Belgium. Partners are VIB, Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel, Université Libre de Bruxelles, University of Hasselt and University of Liège.

The mission in Belgium is to coordinate these universities and unite them into an interconnected infrastructure. This will make it easier for scientists to find and share data, merge expertise and agree on best practices. Ultimately, it will help us gain new insights into how living organisms work. Frederik Coppens is responsible for this task, he’s a staff scientist at the VIB-UGent Center for Plant Systems Biology.

Frederik: “I have noticed several times in the course of my work that many of our colleagues are not familiar with data analysis because they have not been trained in it. However, the fact that they have to assess whether research results are reliable and relevant makes it a vital skill. At the same time, computers are struggling to interpret external data as well. There is truth in the saying that bioinformaticians spend 80% of their time converting between different data formats. Rather than building scripts for ‘housekeeping’, we’d all like more time to spend on the really interesting stuff. That is exactly what ELIXIR is aiming for.”


Kim De Ruyck on ELIXIR Belgium: “building a network of bioinformaticians”
The ELIXIR Belgium lead team includes Yves Van de Peer, Frederik Coppens, Lieven Sterck and Kim De Ruyck
from the VIB-UGent Center for Plant Systems Biology, and Alexander Botzki from the VIB Bioinformatics
Core. Kim is responsible for coordinating ELIXIR Belgium’s activities across the country.

Kim, can you give a couple of examples of projects at VIB that have been carried out under the umbrella of ELIXIR?
Kim: “Last year, we organized the ELIXIR Belgium training meeting, with 20 participants of 13 universities
and research centers, to kick off the activities of the training platform of the Belgian ELIXIR node. There, we
organized a nationwide bioinformatics training network. In the meantime, four ELIXIR trainings are planned
for this year. And last February, the ELIXIR Belgium launch event took place in Ghent, where we invited
researchers, policy makers and funders. ELIXIR Belgium also contributed to ELIXIR’s training portal TeSS.
This platform allows to disseminate, discover and package training resources, training materials and events.
All trainings organized by the VIB Bioinformatics Core are available in TeSS.”

How are we exactly pooling together resources in Belgium?
Kim: “A good example of pooling and sharing data is our involvement in the Beacons Project. Beacons allow
researchers to query individual datasets to determine whether they contain a specific genetic variant of
interest. For example, they can ask Beacons simple questions like ‘Do your data resources have genomes
with a specific allele at a certain position?’ The ELIXIR Belgium Beacon, also known as NGS-Logistics, provides
access to exome variant frequencies from patients with rare genetic disorders. But, most importantly, we’re
also building a network of bioinformaticians in Belgium. This allows us to address common challenges.”

What are the next steps for ELIXIR Belgium?
Kim: “Well, we just got started and currently I am the only person working full-time for ELIXIR Belgium. But
thanks to recent Flemish funding, we are able to expand our team with two software developers, and we
are in the process of hiring an ELIXIR Belgium trainer. He or she will help in organizing and providing ‘train
the trainer’, ‘train the developer’ and ‘train the researcher’ trainings and workshops. We also aim to expand
the involvement of our partners and to increase the portfolio of services offered by the Belgian ELIXIR node.
And to link with the industry, we are organizing an ELIXIR Innovation and SME forum on Food and Nutrition
Data targeting the microbiome.”

Go back to the overview '​Big data'

From left to right: Lieven Sterck, Frederik Coppens, Kim De Ruyck, Yves Van de Peer and Alexander Botzki