Researching in Silico

The European Media Laboratory (EML) in Heidelberg was listed in the Süddeutsche newspaper as one of "the world's top ten dream research locations," along with the likes of the Keck Telescope in Hawaii. But if indeed EML's home, the former residence of Nobel laureate Carl Bosch in Villa Bosch [pictured below, left], is not an address to be sniffed at, its innovative research vision may be what makes it really attractive for young researchers.

“Think beyond limits” is EML’s motto, explains Professor Andreas Reuter, EML’s scientific and managing director (pictured below, right), and indeed accurately characterises a pretty unique and progressive research institute. EML was established in 1997 as a private company (GmbH) by Klaus Tschira, a founding member of the software giant SAP.

Physicist Tschira had the desire to support innovative blue-sky and applied research based on IT. Last year, EML split into two branches: EML GmbH, which conducts applied research (with a view to product development), and EML Research, a nonprofit entity with a basic research profile. According to Reuter, EML Research "uses IT to solve real scientific questions."

The combined EML houses six research groups with surprising diversity. However, Reuter explains that all EML projects have a core objective in common: to “develop technologies and design software with a long-term potential that are useful and nonintrusive to the user, but we are not developing IT for its own sake.” The most obvious examples may be projects conducted by the Personal Memory group at EML GmbH, where intuitive information systems that have revolutionary human-technology interaction, such as SmartKom, are being built.

EML Research consists of five research groups, three of which are focusing on fundamental biology questions, and (as a former experimentalist) when I walked into the "lab", I was struck by the lack of reagents lying around. No cell culture lab, no microscopes. But that is not to say that the researchers are developing software in a purely abstract context. The Bioinformatics Research Group leader, Dr. Ursula Kummer, explains that her team develops methods and software to answer "real-world problems."

Such computer modelling, which falls under the realm of "virtual biochemistry", can simulate, for instance, the biochemical pathways within the living cell. Kummer's group is working in an area that has intrigued biochemists for decades--the role of calcium in hormone-induced cell signalling. So in which ways does the approach of researchers in computational biochemistry differ from those in a more traditional biology field?

Andreas Reuter

"Experimental biologists often think in static terms and tend to look at biological processes in isolation, whereas our approach is to think in more dynamic terms," explains Kummer. But in no way does she dismiss the "wet" lab approach, and she stresses that it is crucial to confirm the results of any modelling study in the wet lab. Although she is sticking to dry science in Heidelberg, her team currently consists of an impressively diverse group including computer scientists, physicists, biochemists, and chemists.

It seems that an interdisciplinary approach is the name of the game and one that Dr. Rebecca Wade also has embraced. Trained in molecular biophysics, Wade heads the Molecular and Cellular Modelling group. They use computational approaches to study macromolecules and their interactions, for example, by simulating how two proteins dock with each other. Wade herself has no formal computer science training, and she admits she has greatly benefited from the in-house programming expertise at EML. In general, she would recommend getting as broad a scientific training as possible at the bachelor's and master's levels, particularly making sure to acquire the necessary mathematical skills.

Molecular Movies Live!

Want to see how a protein unfolds or how a drug docks into a target protein binding site? Then click onto the Database of Simulated Molecular Motions (DSMM) to see "movies" of cellular processes happening before your eyes. The purpose of this database is to provide an easily searchable source of information showing biomolecular motions that have been generated by computer simulation. EML researcher Dr. Ting Wang--pictured below--has set up and maintains this service, which is freely available to all researchers (submissions are also welcome).

Wang is part of Rebecca Wade’s team, and she is developing software to predict and simulate biomolecular interactions. Wang studied chemistry and computer science at the University of Science and Technology of China in Hefei and went on to do her PhD at the Institute of Process Engineering in Beijing. She has no formal biology training, but she finds biological processes a fascinating challenge and sees computational biology as a field with plenty of opportunities.

Take at a look at the array of molecular movies on the DSSM site and visualise processes such as protein folding and protein docking (requires MPG video player software).

If making molecular movies comes across as ambitious, so will the aims of the Scientific Databases and Visualization group, headed by Dr. Isabel Rojas, which focuses on building scientific databases to organise biological data. The process is not in the least straightforward, as her team wishes to build a system that can offer a lot more than a "normal" data repository. They are striving to build databases that can "capture the underlying biological concepts" and can be used as tools in their own right to analyse data. This type of field delves into the realms of computer linguistics and abstraction. Rojas's team consists mainly of biologists, but she also has a chemist and computer scientists on board.

The extent to which researchers work on cross-disciplinary projects is something I am totally impressed by. Therefore, I ask the question, what does it take to enter the type of research conducted at EML Research? All group leaders stress the need for interested researchers to have a broad background so that the interdisciplinary research mode is not totally alien. Although Kummer has observed "a reverse in the trend of over-specialisation over the last decade," she says "it is still hard to find the right person." She stresses that candidates interested in an interdisciplinary research project should be flexible and willing to learn a lot of new skills and knowledge to be attractive on the job market. As for Rojas, she feels that the key to working on such interdisciplinary projects is to keep "an open mind."

With a staff of just over 40, Reuter isn't envisioning a major expansion for EML Research but instead, "very moderate growth." He values the present size and intimacy of EML Research and says, "we focus on our core competencies and then build on collaborations for further expertise." Wade sees EML Research as "very different to a traditional environment," which has almost a "family-like atmosphere"--she feels the interdisciplinary nature of the institute has forced all researchers to develop excellent communication skills.

However, the small size doesn't mean that there are no opportunities for young scientists wanting to work at EML Research, particularly in systems biology. In fact, earlier this year the Center for Modelling and Simulation in the Biosciences (BIOMS) was established in Heidelberg and comprises of a collaboration between EML Research, the European Molecular Biology Laboratory (EMBL), the German Cancer Research Center (DKFZ), the Max Planck Institute for Medical Research , and the Interdisciplinary Center for Scientific Computing at the University of Heidelberg. Research at BIOMS will focus on modelling and computer simulation on biological systems. By using a systems biology approach, researchers deliberately move away from the classic reductionist manner of looking at molecules in isolation to study biological systems in their entirety.

The centre is being funded by the Klaus Tschira Foundation and the German federal state of Baden-Württemberg. Funding will be exclusively used for the promotion of young scientists. Postdoc positions (for up to 3 years) are available and the selection process will take place three times a year; the next selection is coming up shortly. More information can be found online.

EML Research receives additional funding from the German Ministry for Education and Research, the European Union, and the German Academic Exchange Service, but the budget is still largely covered by the Klaus Tschira Foundation. This stability puts the institute in the fortunate position of being able to undertake such futuristic projects in an economic period where funding for IT-based research could be difficult.

Although Reuter admits that developing a complete computer simulation of a functioning cell--a process that all EML life sciences researchers are already contributing to--is still a good bit away, he sees the long-term fruits of their research to be "of huge relevance to understanding fundamental biology to drug design."

Editors note: For those interested in seeing what exciting developments are going on in the systems biology field, check out the 5th International Conference for Systems Biology (ICSB), which is being held 9 to 13 October 2004 in Heidelberg.

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