Junior professor Dr. Stefan Günther from the Institute for Pharmaceutical Sciences at the University of Freiburg has a long-standing interest in computer sciences and is now developing software to model three-dimensional protein structures. This enables him to predict interaction mechanisms between therapeutic substances and cellular enzymes.
Should they work with a long-standing cooperation partner or should they set up another company that was the decision faced by the staff of the Discovery-IT department of Nycomed formerly ALTANA Pharma in the spring of 2007.
In the next winter semester Freiburg University will offer a new masters course in Bioinformatics and Systems Biology. The objective of the two-year course is to train experts at the interface of the computer sciences and life sciences.
The new RNA Bioinformatics Center (RBC) is a joint project of the Universities of Freiburg and Leipzig as well as the Max-Delbrück Center Berlin. It is one of six performance centers selected for funding by the Federal Ministry of Education and Research (BMBF) and will receive 3.3 million euros in the next five years. It is part of the project “German Network for Bioinformatics Infrastructure,” which was launched on 1 March 2015.
The German Network for Bioinformatics Infrastructure, de.NBI for short, is a successful model for infrastructures in the life sciences and biomedicine that is currently being expanded. The network, which was established in 2015, will benefit from more hardware, more staff, more projects and its own cloud. It has also joined the European ELIXIR network.
Bioinformatics methods are important tools for the classification of protein sequences. Prof. Dr. Tancred Frickey, Professor of Applied Bioinformatics at the University of Konstanz, has developed a programme that enabled him to classify the AAA ATPase protein family. CLANS software can also be used to visualise the similarities between film actors who have played roles in the same genre category.
Metabolism stress response and gene expression are all controlled by regulatory networks in living systems. Well-known regulators are proteins which function as enzymes chaperones or transcription factors to regulate numerous processes. Less well-known are RNA-molecules which also regulate a multitude of processes small RNAs or sRNAs. Dr. Jens Georg from the Department of Genetics and Experimental Bioinformatics at the University of Freiburg has made it his goal to identify these sRNAs and their interactions and physiological functions in bacteria. In order to do so along with colleague he has developed a new computer-assisted tool the online software CopraRNA which can be used to make extensive predictions about the small RNAs.
The Tübingen-based software company is one of 750 members listed in the first “Lexikon der deutschen Weltmarktführer” (Encyclopedia of German Global Market Leaders). The encyclopedia was presented in Schwäbisch Hall at the end of January 2011.
Dr. Carsten Daub a German bioinformatician who first studied chemistry at the TU Berlin did his doctoral degree in 2004 at the MPI of Molecular Plant Physiology in Potsdam Germany and after a two years post-doctoral training at the Karolinska Institutets Center or Genomics and Bioinformation in Stockholm Sweden joined the Genome Sciences Center at RIKEN in April 2006 on a five years contract.
Individual patients metabolise certain drugs in very different ways some patients metabolise drugs well and others do not respond at all. The difference in individual patients ability to metabolise drugs depends not only on environmental influences but also on genetic factors which means that the sequencing of the human genome has become a major prerequisite for the application of personalised medicine. In the following interview Dr. Jens Hoefkens head of Genedatas Expressionist Business Unit explains why next generation sequencing enables patients to be treated more efficiently and how information technology can contribute to identifying potential adverse drug effects at a very early stage.
Systems biologists and bioinformaticians from all over the world met in the Heidelberg Institute for Theoretical Studies in early September 2011 with the aim of coordinating the various community standards and formats in systems biology and related fields. The “Computational Modelling in Biology Network” (COMBINE) aims to advance international understanding and cooperation in the field of systems biology.
The use of modern research methods in the natural sciences generates increasing amounts of data, which can often only be analysed using special software. The INCIDE research centre at the University of Konstanz provides data processing services that facilitate the development and adaptation of software programmes for use in the life sciences. The INCIDE scientists work in close collaboration with life scientists. In future, this successful concept will also be used for external projects.
The biologist Prof. Dr. Stefan Rensing from the University of Freiburg has been involved in introducing the use of computers to the life sciences from the very beginning. His analyses of the moss genomes now help to close an important gap in evolutionary research how did algae become land plants?
Every February, the World Health Organisation (WHO) publishes recommendations on the composition of influenza virus vaccines for use in the upcoming influenza season. The WHO’s decision is based on observations and laboratory tests as well as experience and intuition. The particular type of influenza virus that is likely to be circulating in a given season has previously been mainly a matter of speculation. Richard Neher from the Max Planck Institute for Developmental Biology in Tübingen, in cooperation with scientists from the UK and the USA, has developed software that takes a less speculative glimpse into the future.
Computer analyses of protein folding have shed light on the evolution of early life on earth. Researchers from the Heidelberg Institute for Theoretical Studies and the University of Illinois, USA, have examined the folding speed of the domains of proteins and found that there has been a trend towards the optimisation of protein folding since their appearance 3.8 billion years ago. 1.5 billion years ago, more complex domain structures and multi-domain proteins emerged and caused a ‘Big Bang’ of proteins.
Databases are classical tools for the collection, administration and presentation of computer data in table form. Tübingen-based Hölle & Hüttner AG has developed a completely new solution – H-Maps: a semantic knowledge matrix that associates and represents information as clearly arranged networks. This gives users a rapid overview and enables them to recognise new relationships.
Germany will contribute another project to the International Cancer Genome Consortium ICGC. Coordinated by the German Cancer Research Center and the University Medical Center Hamburg-Eppendorf physicians and molecular biologists will now start to investigate the genetic causes of early prostate cancer.
The combination of a newly developed bioinformatic model and experimental data provides new insights into the causes of Alzheimers disease. Researchers found that whilst the activity of a particular enzyme is reduced specific nerve cells are able to counteract this deficiency by rerouting the metabolic fluxes.
Alexandros (Alexis) Stamatakis heads the new research group “Scientific Computing” at the Heidelberg Institute for Theoretical Studies (HITS) – Software and supercomputing for large-scale biological data analysis.
It has now become clear that non-coding RNAs are the puppeteers in cells. Prof. Dr. Rolf Backofens team at the University of Freiburg is developing an indispensable tool for doing just this in the form of computer programmes that generate two-dimensional structural models of these tiny all-rounders.
“Omics” is a current buzz word used to describe comprehensive investigations in many areas of the life sciences. In practice, omics refers to fields of scientific study that involve a huge number of experiments and even more data. Evaluating and managing all the data within a fixed period is a huge challenge for most researchers working on their own. It was to address these issues that the Quantitative Biology Center – QBiC for short – was established at the University of Tübingen in 2012. To date, the QBiC is the only bioinformatics core facility in Germany. It offers scientists from different disciplines support in carrying out all types of high-throughput analyses. The centre is also the only one that provides professional support from initial planning of experiments to final analysis.
The use of cutting-edge genomics, proteomics and metabolomics methods generates ever-increasing amounts of data in ever decreasing timescales. Special mathematical and computational methods are required for deducing relevant information from specific patterns. The data mining specialist Karsten Borgwardt from Tübingen is developing such methods for specific application in the life sciences.
Bacteria adapt quickly to their environment and also to antibiotics. Many of the antibiotics used to treat bacterial infections have become ineffective as a great many bacteria have become resistant to them. Freiburg-based FreiBiotics GmbH is looking for completely new classes of antimicrobial substances. A screening method that has been developed over the last few years based on biosensors makes the identification of new substance classes more efficient at the same time as reducing the costs associated with their development.
Scientists at the BioQuant centre in Heidelberg have developed an automatic particle tracking method that can be used for time-resolved two- and three-dimensional microscope image data. This powerful computational method achieved the best overall result in an international competition that compared different methods for the quantitative tracking of the position of moving biological particles.
cubuslab, a start-up company that was spun off from the Karlsruhe Institute of Technology in March 2015, has developed a technology to connect different types of laboratory equipment, from precision balances to analytical instruments. The technology is aimed at automating workflows and connecting and storing data in an electronic laboratory notebook.