07.07.2022

Data Science close to the lab

The Tübingen Center for Quantitative Biology (QBiC) celebrates its 10th anniversary

Since 2011, the Center for Quantitative Biology (QBiC), as a Core Facility of the University of Tübingen, has supported researchers from the life sciences in planning experiments and analyzing the data generated in the process. At QBiC, all large amounts of data from the high-throughput technologies on campus come together. The center pools the know-how of a total of ten Tübingen institutions that have excellent equipment and expertise in biomedical analytics and bioinformatics. Johannes Baral spoke with Prof. Dr. Sven Nahnsen, bioinformatician and director of QBiC, about the past and future development of the Core Facility as well as about the upcoming Biomedical Data Symposium celebrating its tenth anniversary on July 8. 

How has QBiC developed in the ten years since its founding?

It was and is an exciting time. We started back then with many different goals. One of the goals was to bring together already existing life science facilities, the Core Facilities, with their services and technologies in favor of a homogeneous appearance. The intention was not to physically bring these Core Facilities together under one roof as a joint facility, but to leave them in their existing research areas, where they work directly at their scientific questions. Rather, the intent was to have a common data and project management approach as a large Core Facility QBiC. 

As research data have become increasingly important, another objective was to annotate and archive large amounts of data from life science research - and to do so in close collaboration with the existing Core Facilities, which generate this data. We started relatively simply and then realized that such an infrastructure could also give us a competitive advantage in attracting future research funding. I think that after ten years we have put this vision into practice. Scientists who need support with sequencing, mass spectrometry, bioinformatics or even just data management, for example, can get it from us from a single source.

Does QBiC also conduct research itself?

Yes, our own research work is primarily concerned with methodological research. That means that we further develop data science methods, which in turn flow into services for researchers. In my opinion, it is very important that Core Facilities have their own research agenda.

QBiC is also funded by the German Excellence Strategy.

The success of the University of Tübingen in the Excellence Initiative, or in the meantime: Excellence Strategy, have helped us immensely. At the same time, the German Research Foundation (DFG) also gave us the opportunity to obtain start-up funding for QBiC from a dedicated Core Facility call. Both then came together in 2011 and 2012. We have positions that are funded by excellence funds, so it is also very important for us to pull together with the other institutions of the university and to keep excellence in Tübingen. Without the Excellence Strategy, it would certainly not have been possible to make QBiC what it is today. And we hope that as a Core Facility we can contribute in return to future successes of the University of Tübingen.

What have been the highlights of QBiC's ten years?

One would definitely have to mention that, together with Medical Microbiology and Human Genetics, we were able to bring one of four national DFG-funded sequencing centers to Tübingen. We have also made some groundbreaking developments in bioinformatics workflows. For example, we created a software framework called nf-core, a technology that is now being used in other Core Facilities around the world. This technology allows for very scalable, reproducible and simple bioinformatics processing of large data sets. This is an nf-core initiative involving several thousand bioninformaticians worldwide. Scientifically, it's a very exciting thing that has given QBiC a lot of visibility. Over the years, other institutions, such as the Robert Koch Institute or the University of Basel, have also repeatedly approached us and asked for support in developing concepts for setting up their own core facilities. 

From which disciplines do the scientists working at QBiC come?

Our core expertise lies in the areas of bioinformatics and software development and in the application area of biomedicine; through our application areas, we are always close to the laboratory with our questions and objectives. To bring the data together, it is essential to work very intensively with colleagues in the laboratory where the data are generated. Data can only be used again if they are fully annotated. That is, when we have recorded all the additional information required in the database, from the initial project description to the description of the samples and the laboratory methods. Only then can we make data usable again for other research projects. 

What services does QBiC offer in detail?

We essentially cover the entire data creation chain. For example, we offer experiment design. Researchers come to us and we design the planned experiment if it fits our expertise with high-throughput technologies. We take care of the metadata collection. So, for example, if someone approaches us with a study on cancer, we capture all the descriptive data in structured data models. That's the first part of data management. The next step is then data generation, which we also offer as a service. However, this does not take place under our umbrella, but via cooperation agreements in partner facilities. Once the data has been generated, data management includes bringing it back to us centrally. Finally, we offer data evaluation. That would be the overall package, from which the researchers can also pick out the individual components.

Who uses the services of QBiC? Is it primarily researchers from Tübingen?

Yes, we created the service facility primarily for Tübingen as a research location. This means that we are primarily for University of Tübingen researchers, for example from the Medical Faculty, but also from the Max Planck Institutes. However, since we have noticed that our offers are of interest beyond this, they are also open to external researchers. And, of course, there are occasionally companies that request our specific expertise for research projects.

What can participants expect at the Biomedical Data Symposium on July 8?

We are looking forward to a very exciting day with five external speakers. Above all, we want to present what QBiC has to offer, what has happened at our Core Facility over the last ten years, and where we want to go in the future. Where are the upcoming big challenges in data management? How do we plan to expand our service portfolio to remain competitive? We will present our own technologies with numerous posters so that visitors can have a look at the spectrum of methods. It will be possible to talk to all QBiC employees on site. The whole event will be accompanied by a scientific symposium with those working in Biomedical Data Science. Among others, Anne-Laure Boulesteix from LMU Munich, who deals with biostatistics, and Cedric Notredame from Centré de Regulatió Genomica Barcelona, who deals with reproducible workflows in research. Finally, Gene Myers from the Max Planck Institute Dresden will give the keynote address. He is a bioinformatician of the first hour, a pioneer of our discipline. Of course, we hope that the participants will stay with us a little longer afterwards to toast 10 years of QBiC. 

What's next for QBiC in the near future? 

We will continue to drive forward the integration of Core Facilities. The Metabolomics analysis unit is very important here. In addition to the focus on omics technologies, i.e. high-throughput technologies, imaging is playing an increasingly important role. Imaging is producing ever greater volumes of data, for example in microscopy or medical imaging. This is a technological mainstay that we will definitely expand. In addition, machine learning is also a big topic for us. Our premise here is to form an interface. We want to prepare research data in such a way that we can access it efficiently using machine learning methods. We see a lot of potential here, for example in the treatment of cancer patients or in antibiotics research. From a purely data science point of view, it will become more important to also integrate external databases with us. This is another area we will be looking at more closely in the coming years.

More information about the Core Facility and the symposium on the QBiC website https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/events/

Johannes Baral