ANALYSIS & OPINION

Systems biology spreads across Europe

23 March 2007



At face value, Bacillus subtilis seems a pretty boring specimen that few would care about. It is not a pathogen, and if it does contaminate food it rarely causes food poisoning. Possibly its only claim to fame is in producing the Japanese delicacy natto, or fermented soybeans.

Not much reason, then, to warrant a multinational research project. Look a bit deeper, however, and the bacteria proves to be highly agreeable to genetic sequencing and manipulation – providing the main focus of a European systems biology initiative spanning nine countries and involving 15 separate research organisations.

BaSysBio (Bacillus Systems biology), launched officially last November, hopes to use Bacillus as a model organism: combining previous data with current experimental research to gain a deeper understanding that can then be transferred to other organisms. Bacillus subtilis could even prove to be potentially useful in its own right, to produce enzymes, metabolites and vitamins for the pharmaceutical industry.

The project will also study Bacillus anthracis, a related organism responsible for anthrax, and Staphylococcus aureus, which causes secondary infections, hoping to understand the infection mechanisms involved and to identify targets for drugs.

The 48-month initiative is one of a growing number of European consortia using a systems biology approach, combining many different disciplines and techniques on a single project. Genedata, as part of its growing consultancy service, is responsible for the coordinating the infrastructure and informatics of the initiative – a considerable task considering the disparate nature of the data and methods involved.

Part of the task will be to tailor existing databases to the challenges of the project. ‘It’s very important to combine the existing data with current experimental data,’ Dr Thomas Hartsch, a scientific consultant from Genedata involved in the project, told scientific-computing.com. ‘There’s a lot of distributed knowledge available, but most is stored in the scientist’s C drive. We must see what’s important, and transfer, integrate and make use of it.’

Genedata’s Phylosopher is the primary tool to enable this, linking relational databases and allowing restrictions to be placed on certain areas. In addition to installing the software and providing extended support, Genedata is also providing training to allow scientists to use the software to its full potential.

‘It is becoming more and more important to integrate workflows into our software,’ said Hartsch. ‘We can learn from the consortia, and hopefully transfer the knowledge back into the pharmaceutical industry.’

Another similar systems biology consortia in which Genedata recently became involved, HepatoSys, has just entered its second funding phase. In the words of Dr Ute Heisner, the project coordinator, it aims to ‘arrive at a holistic understanding of the life processes of liver cells, and to make them available in silico.’

The initiative combines medical doctors, chemists, biologists, process engineers and informaticians. ‘Obviously language is a bit of a problem,’ Heisner told scientific-computing.com. ‘If you work on single topics, it’s not so much of a problem, so I visited all the working groups and decided on specific tasks.’

Obviously increased communication and cooperation is the key benefit of such consortia when generating new ideas. ‘Two of our projects – endocytosis and cell biology - work hand in hand. It just wouldn’t be possible if they weren’t in a network.’

Dr Thomas Hartsch agreed: ‘It’s the academic community that will benefit most. It will be very interesting to see how different labs will reach out and work together.’