What do bioinformatics researchers actually do

Bioinformatics: detective work in the genome

bmbf.de: At least since the decoding of the human genome, computer science methods have become an integral part of biology. Is bioinformatics the Swiss Army Knife in the life sciences?

Alexander Goesmann: That would be too brief, but it is an interesting comparison. Experimental researchers send us their raw data, and we then provide interpretable results. Seen in this way, bioinformatics is a useful tool for evaluating large amounts of data. In addition, bioinformatics has developed strongly in the last 20 years and has become a separate scientific discipline with numerous specializations. In addition to data evaluation and visualization, the aim is to find completely new solutions using methods from mathematics and computer science.

How important is biological knowledge in this process?

The biological knowledge is just as important as the theoretical and technical disciplines - it is and will remain a very interdisciplinary subject. You have to understand how biological systems work and how experimental data are generated in order to develop tailor-made tools and use the programs correctly. This is the only way to end up with a solution that creates real added value.

What does this added value look like in concrete terms?

A current example is the corona virus, which is currently spreading worldwide. The genetic makeup of viruses and bacteria is constantly changing. Bioinformatic analysis can be used to determine where the virus first appeared and how it spread from there. Changes in the genome of the virus can also indicate an adaptation to changed environmental conditions or other hosts. The current virus is also believed to have its origin in wild animals. Another example is the emergence and spread of antibiotic resistance in bacteria.

So bioinformatics is a lot of detective work.

Yes, but we go one step further. In everyday clinical practice, bioinformatics analyzes will in future provide specific support to doctors in their treatment. If you know beforehand whether certain drugs are working or not, you can save the patient from exhausting trial and error and instead treat them specifically with the right drug, for example a suitable antibiotic. Unfortunately, it is becoming increasingly difficult to find effective antibiotics that can still be used for serious bacterial infections. Hardly any new antibiotics have been developed in recent years and resistance has continued to spread.

Will all available antibiotics soon be ineffective?

I don't want to hope so. With new methods we try to look deeper - at the level of the genetic material and the regulation, i.e. the activation and deactivation of cellular processes. There we are looking for targets for alternative treatment routes and the development of new drugs. If you better understand the defense mechanisms of bacteria, you can find points of attack for new antibiotics.

What does your work look like in concrete terms?

In many cases we receive the experimental raw data and then try to track down particularly interesting, functional elements in the genome. In the case of bacteria, for example, we are looking for genes that convey antibiotic resistance. With our software platform, this bioinformatic processing runs completely automatically. At the end there is an interactive visualization. Medical microbiologists can then see at a glance which resistances the bacteria carry and which properties of the germ could be relevant for its spread and thus also for its containment.

The BMBF has been funding the German network for bioinformatics infrastructure (de.NBI) for five years. What has changed for research as a result?

No researcher wants to reinvent the wheel five times, but rather to carry out high-quality analyzes in a targeted manner. The focus of the network is therefore clearly in the service area. Users can now download over 100 bioinformatic tools free of charge or use them online and learn how to use them in individualized training courses. With the network's cloud, you can also work in parallel on several hundred computers free of charge, thereby significantly shortening the time to evaluation. In today's research work with ever larger data sets, it is important to get the results quickly. In addition, the enormous amounts of data can be stored in the cloud and shared by research teams in different locations.

Are these amounts of data still accessible to humans?

Just recently, together with students, I worked out how high the pile would be if the human genome were printed out on A4 pages. The result was a height of almost 74 meters. That is higher than the Victory Column in Berlin. The challenge, however, is not just the amount of data. It is of no use if I know all the letters but cannot read and understand the text. For the interpretation of the data we need bioinformatic programs such as those made available by the network.

Is the network well received by the science community?

Yes. We now receive almost half a million inquiries per month across the network. In the case of difficult problems, we also offer close scientific collaborations. The service and performance centers spread across Germany now cover a very wide range of topics. And if there is still no solution, we will look for new approaches together. I think that the network, with its various services and expertise, could well be described as the Swiss Army Knife in the life sciences.

Thank you for talking to us, Mr. Goesmann.

Five years of the German Network for Bioinformatics Infrastructure

With the targeted establishment of the "German Network for Bioinformatics Infrastructure - de.NBI", the Federal Ministry of Research wants to support researchers in the life sciences in the analysis of large amounts of data. The aim is the effective use of existing data and the efficient use of future technologies and coordinates the network's existing expertise and resources. A major focus is on numerous training courses and advanced training courses on the use of the bioinformatics tools provided. In addition, the development of a cloud began at the end of 2016. This means that the research groups now have sufficient computing capacity to process their Data available free of charge. The network will receive a total of around 80 million euros in funding until the end of 2021.