Bioinformatics: Bioinformatics Central


If you want to learn French, live in France. Total immersion is a great way to learn languages and if you want to try the same trick for bioinformatics, you could do worse than spending some time at the European Bioinformatics Institute (EBI). The intensely interdisciplinary and international EBI welcomes people from specialties ranging from biology to chemistry to physics to computer science. "We take a lot of people pretty cold, who've never done bioinformatics," says Graham Cameron, joint head of the EBI. But unlike languages, which change relatively slowly, bioinformatics moves fast, so you'll need to be on your toes. "It's a very tough, cut-throat field," says EBI research group leader Christos Ouzounis, "and the skills you develop today are useless tomorrow."

The EBI, an outstation of the European Molecular Biology Laboratory (EMBL), shares its rural Hinxton site, south of Cambridge, UK, with the Sanger Centre and the Medical Research Council Human Genome Mapping Project Resource Centre. But despite such pleasant distractions as tennis courts, football and cricket pitches, and the largest concentration of computational biologists in Europe, if not the world, few people stay long.

Graham Cameron, joint head of EBI

Three 3-year contracts are the maximum under EMBL policy, which only allows for a very small permanent staff. And after completing their thesis, EMBL Ph.D. students must move on. As an international organisation, its duty is "to take people in and give them the opportunity to progress, and then pass them back to their own countries," explains Cameron.

Along with research and supporting the commercial sector, training is an important part of EBI's mission, and there are many opportunities to spend short periods at EBI. Postdoc fellowships under the EU Training and Mobility of Researchers programme last 2 years. There are summer placements, mainly taken up by MSc students, to do 3-month projects. And a visitor programme allows visiting researchers to spend between 2 weeks and 3 months at the EBI. The short stays increase the pressure on those changing fields. Ouzounis, who also oversees postdoc training at EBI, points out that "it's very tricky to be productive" in this short time frame when learning a new discipline.

The constant turnover, steep learning curve, and pressure to produce make for a "very intense, very specialised environment," maintains Geoff Barton, who leads a research group at the EBI. But that can be a good thing. "The advantage, if you're into bioinformatics, is that there are lots of people coming through," he says. EBI Ph.D. student Anton Enright agrees and tells Next Wave that he chose EBI precisely because of the huge number of visiting scientists and the opportunity to meet people with diverse skills.

The European Bioinformatics Institute

With the completion of the first draft of the human genome, expansion is on the cards at EBI. "This institute should treble in size," says Barton. EBI already has planning permission for a second building of the same size next door to the existing premises. Assuming funding can be found, there should be a steady demand for data curators and database programmers to help develop and maintain the three major biological databases kept by EBI for use by the worldwide scientific community.

Who do they hire? "The most typical entrant to the EBI has some kind of second degree," says Cameron, who adds that teams are often made up of people from a mixture of backgrounds. Ouzounis, for example, has a background in protein structure prediction, but other members of his group come from chemistry, genetics, physics, genomics, and computer science. Kirill Degtyarenko, a curator on the protein sequence database SWISS-PROT, says that curators are usually biologically trained, while programmers tend to come from a physical sciences background making for "a good balance."

Maria Garcia Pastor, one of six curators on the nucleotide sequence database, came to the EBI direct from her biology degree. In a typical week she'll handle more than 120 new submissions and make updates to old entries already in the database. It's a fast-paced job. Now that submitting data to central collections is often a prerequisite for publication, she tries to turn each submission around in a maximum of 2 days. Pastor must also negotiate with scientists to get the information into a mutually agreeable form and stay up to date on current technologies. "If you're doing something like running a database service, you've got to stay state of the art," Cameron says. "That means you've got to look at what new computer technologies are coming along ... working out how you'll be running your service next year and the year after."

Degtyarenko knows how challenging that can be. He is currently integrating existing enzyme databases into an expanded database that incorporates more detailed information. "The main problem is inconsistencies," he explains. "People use different names for the same thing." Degtyarenko sees himself as a housekeeper for the biological sciences. "Sometimes I don't feel that [what we do is] research," he says, but he believes that it's just as important. "Other people will base their results on our job as well as the experimentalists' job," he asserts. "What we do doesn't create new information," he explains, it "reduces noise" and turns mere information into knowledge.

Serene surroundings for bioinformatic research

A shared passion for bioinformatics and the sheer internationalism of the staff (around 25 nationalities are represented) make for a great working atmosphere according to staff and students. Arne Stabenau, a scientific programmer from Germany in the Ensembl group, has only been at EBI for 7 months and is finding settling in to a new country difficult. "I don't get any jokes," Stabenau tells Next Wave, nor does he like the notoriously bad British weather. But with 25 nations represented at EBI, he never has to look far to find a sympathetic ear. "The good thing is you can always find another German to speak to," he says.

So, what of the future? Bioinformatics is a growing area. "If all we needed to do was sit still, we'd be quite [financially] secure," says Cameron, who explains, "it's always difficult to get funds together in Europe," because "every time you try to raise funding for something you have to go and convince 15 different nations." Cameron estimates that the EBI probably needs an annual budget of at least three times its current allocation from the EMBL. He has a challenge for the policy-makers. "The life sciences are doing things which are really going to change the quality of life, and I think that that warrants more investment."

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