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After Two Years on the Brink, EMBOSS Project Secures Long-Term Funding From UK s BBSRC

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Plans are underway to celebrate the tenth birthday of the EMBOSS software package this summer now that its developers have received word that their funding is secure for at least three additional years — a decision that ends two years of uncertainty around the popular open source bioinformatics suite.

Earlier this week, the European Bioinformatics Institute announced that the UK's Biotechnology and Biological Sciences Research Council had agreed to support the project. While the amount of the funding was not disclosed, project leader Peter Rice said that it is enough to support two developers at the EBI, in addition to himself, for three years as of May 1.

But the funding means more than just three jobs. Rice told BioInform that the support guarantees that the core software will remain stable, which should encourage developers from academia and industry to begin contributing to the open source project and eventually expand its capabilities.

"We hope in coming years that we'll have a lot more outside collaborators," Rice said. "Obviously, nobody wanted to collaborate too much if we could disappear in a few months. It wasn't a great time to set up collaborations. … Now we'll be really looking to see who'd like to use EMBOSS as the basis for development."

Since the UK's Medical Research Council in 2004 closed the bioinformatics division of the Rosalind Franklin Center for Genomics Research, which housed the bulk of the EMBOSS development team [BioInform 05-17-04], the three core developers have managed to keep the project alive through "interim" funding from the EBI, but the effort has largely been "on hold," Rice said.


"Obviously, nobody wanted to collaborate too much if we could disappear in a few months."

The impact of this holding pattern on users and collaborators is unclear, but it appears that many remained loyal to the effort despite the funding uncertainty. Rice noted that letters of support from dedicated EMBOSS users across the world helped convince BBSRC to fund the project. In addition, he said that many big pharma users that make up the EBI's Industry Program have continued to use the software because they have a great deal of in-house bioinformatics expertise and would have been able to continue maintaining the suite internally even if the funding ran out. Smaller biotech firms and academic users were more likely to explore other options over the past two years, Rice said, "but we expect that they'll come back to EMBOSS."

Rice said that he and the two other EMBOSS developers now at EBI — Alan Bleasby and John Ison — have a contract with the Cambridge University Press to write three books targeted toward different EMBOSS user communities: software developers, database administrators, and lab biologists.

Online versions of each of the books will also be available as user guides through the EMBOSS website (http://emboss.sourceforge.net/index.html), and Rice said he expects the books to expand usage of the software suite in all three areas.

As for future development plans, Rice said that EMBOSS 4 is scheduled for release on July 15. The release will include a "major cleanup" of the internal library code, which the team has been planning to do for some time, "but we couldn't really implement because if the funding suddenly got cut off, we didn't want to leave the code in a mess where nobody understood it," Rice said.

Other features in the upcoming release include updated database indexing to account for changes in the EMBL nucleotide database scheduled for June (see briefs, this issue, for further details).

EMBOSS 4 will also include metadata for interfaces and service wrappers and improved output formats.

Longer term, Rice said he'd like to see the effort move beyond sequence analysis to include modules for microarray analysis, proteomics, genetics, and other applications — a goal that will likely require collaboration with external groups. A Windows version of the software suite is also on the horizon, he said.

Rice said that the core developers also plan to establish stronger ties with commercial users who have developed interfaces to EMBOSS or who have embedded it in their own products. "We can work with them and tell them what's happening in new releases ahead of time, or if they've got things that they particularly depend on, we can make sure that we test against their interfaces and make sure that we don't break things," he said.

Rice said that he has already heard from several firms who are interested in partnering with the effort, although he declined to name specific companies.

More immediate plans include the project's tenth birthday party, Rice said, though he added that a date has not yet been set for the celebration. "We've put that on hold until we had the new funding," he said.

— Bernadette Toner ([email protected])

BBSRC Sets Aside $18M in 'Sustainability' Funding for Bfx, other Resources

EMBOSS is among a handful of bioinformatics projects, including BIND, the GDB, and SwissProt, that have had to struggle to secure long-term funding — a persistent challenge for resources that have matured beyond the priorities of funding agencies that support cutting-edge science.

At least one funding agency is taking steps to address that issue, however. Nigel Brown, director of science and technology at the UK's Biotechnology and Biological Sciences Research Council, told BioInform that the council has recently decided to establish "a new funding stream that is specifically to deal with the sustainability of bioinformatics and other biological resources."

Brown said that the BBSRC is "well aware" of the importance of bioinformatics software and databases — as well as other biological resources like culture collections, seed banks, field sites for agricultural research, and the like — and has set aside "just over" £10 million ($18 million) for the program. The first call is expected to go out in the next few weeks.

While "things like EMBOSS and other bioinformatics and genomics resources" will likely seek funding from the program in the future, Brown said that BBSRC's recent decision to fund the software project did not fall under the initiative "because we hadn't yet made the call for proposals."

The funding for EMBOSS "was in recognition that it's a core international facility" and was subject to the BBSRC's "normal peer review process," he said.

"What we've decided to do is to fund the core facility to maintain it over the next three years and ensure that it is there and able to deliver," he said. Nevertheless, he noted, "I can't promise the future funding of EMBOSS."

Even under the new sustainability initiative, projects will have to compete for funding, Brown said.

"As a funding agency, of course, we're very conscious that there are a huge number of resource requirements … and we could spend a vast portion of our budget just maintaining them and not doing any new science," he said. "We just have to get that tension right."

— BT

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