European bioinformatics grid receives 8 million Euro
The Commission of the European Union has awarded 8.3 million Euro to a pan-European task force who will improve access to biological information for scientists throughout and beyond Europe. The EMBRACE Network of Excellence, which encompasses computational biologists from 17 institutes in 11 countries and is coordinated by the European Bioinformatics Institute’s Associate Director Graham Cameron, will use these funds to simplify and standardize the way in which biological information is served to the researchers who use it.
Scientists now depend on databases to access the avalanche of information that they produce. For example, geneticists are trawling through the human genome for genes that are involved in diseases. Data providers put a huge amount of effort into providing data resources that are comprehensive, user-friendly and cross-linked to other databases; but different data providers use different methods. This means that a researcher might have to search ten or more different databases to find all the information pertaining to a particular set of candidate genes. If they’re doing these kinds of searches on a regular basis, they’ll want their own local copies of the databases. Maintaining up-to-date and fully functioning versions of all those databases and the tools to search them is a huge and complex task.
Vincent Breton (CNRS, Clermont-Ferrand, France), a member of EMBRACE’s Executive Board, describes the problem as analogous to the use of electrical items before the electrical grid. “You didn’t know whether your gadget’s plug would fit the socket,” he says.
EMBRACE will turn the relationship between user and provider on its head by enabling data providers to provide well-defined interfaces to their databases that will conform to the same standards, essentially creating a ‘data grid’ – the EMBRACEgrid – that will allow users to make the most of dispersed data resources.
To ensure that EMBRACE’s efforts are immediately useful to biologists, Europe’s most heavily used biomolecular databases and tools will be integrated into the EMBRACEgrid. A ‘technology watch’ will ensure that the EMBRACEgrid doesn’t become locked into technology that is quickly superseded. The grid will also receive regular workouts using test problems, such as identifying candidate genes for a disease or linking viral mutations to their ability to cause disease. Disseminating information about the EMBRACEgrid will be vital to ensure that scientists throughout Europe not only use the new technology, but also help to expand the capabilities of the EMBRACEgrid by ‘grid enabling’ their own data resources.
“Many elegant and powerful computational biology tools are under-utilized,” says EMBRACE Executive Board member Erik Bongcam-Rudloff (University of Uppsala, Sweden). “EMBRACE will allow us to unlock their potential by standardizing access to them.”
The nucleus of this cell fluoresces in bright green thanks to GFP-labelled nucleoporin proteins. EMBL scientists use engineered nucleoporins as 3D reference standards to improve super-resolution microscopy.