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Optimistic EMBOSS Development Team Prepares for Spring Release of Version 3


Despite a funding crisis that has left several of its core developers searching for new jobs, the European Molecular Biology Open Software Suite software package is on track for a new release sometime in early 2005.

Peter Rice, group leader at the European Bioinformatics Institute and EMBOSS co-founder, told BioInform last week that development on the open source package is progressing, and that he and his colleagues are “optimistic” that new funding for the project will be secured in the near future.

In March, the UK’s Medical Research Council announced that it will shut down the bioinformatics division of the Rosalind Franklin Center for Genomics Research — which had hosted EMBOSS — by July 2005. Alan Bleasby, EMBOSS coordinator and head of the proteomics applications group at the RFCGR, told BioInform at the time that the decision would leave around 20 people in the bioinformatics group without jobs and halve the EMBOSS core development team [BioInform 05-17-04].

Bleasby and another EMBOSS developer are still at the RFCGR, and two EMBOSS developers are still funded under another grant from the UK’s Biotechnology and Biological Sciences Research Council, but Rice said that as the months drag on without securing a funding source after July, “We’re going to start getting nervous fairly soon.”

Rice added that there are a number of reasons for optimism, however. For one thing, the EBI has committed to providing half of his salary toward EMBOSS development, with the other half reserved for the e-science and grid computing projects that are the primary responsibility of his group.

In addition, upwards of 900 EMBOSS users have responded to a survey the group sent out by e-mail earlier this year (also available at Rice said the survey results have been largely positive, and should provide ample justification for the MRC, BBSRC, and other funding groups to continue supporting the project. He said he heopes to get at least 1,000 responses before submitting the results to the funding bodies.

Based on the preliminary results, 90 percent of EMBOSS users consider the resource to be “valuable,” and, not surprisingly, 90 percent also said that the resource should remain free. Rice said that around 70 percent of the respondents felt that EMBOSS should be supported by public funding, while only 15 percent recommended commercial sponsorship for the software package.

Rice said that the team wouldn’t rule out some form of commercial sponsorship, noting that “there are a couple of companies interested in working with us, but there is nothing definite yet.”

Of the respondents so far, around 70 percent described themselves as end users, rather than developers, Rice said, and around 18 percent said that they use the package as the basis for their own software development.

Rice said that some responses will help guide future EMBOSS development. One surprising finding, he said, was that around half of the current users run EMBOSS on Windows, although since many respondents use multiple operating systems, the majority still run it on Unix. Nevertheless, Rice said, “we may have to look at providing a better Windows client.”

For the version 3 release, slated for some time in early 2005, Rice said that the team is aiming for XML support, and better support for workflow packages like EBI’s Taverna and web services systems like BioMoby. Improvements are also planned for the graphics library, the database indexing system, and specific components like the Phylip phylogenetic tree package.

— BT

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