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New Funding for EMBOSS Bioinformatics Tools



EMBOSS, the European Molecular Biology Open Software Suite, has received new funding from the Biotechnology and Biological Sciences Research Council (BBSRC) in the United Kingdom that ensures its survival as an open-source utility, at least for the next three years.

The fate of the EMBOSS project had been in doubt for the past two years, following the closure last summer of the Rosalind Franklin Centre for Genomics Research (RFCGR), which had hosted the project.

“We’re delighted that the BBSRC has recognized EMBOSS as an important tool for molecular biology,” said project co-founder Peter Rice in a statement. “The EMBOSS user community has been very patient, and it highlights a great benefit of open source software that even users in industry have continued to rely on EMBOSS despite the uncertainty about its future. This simply could not have happened if EMBOSS had been a commercial package under threat.”

EMBOSS is an open-source suite of some 300 applications for molecular biologists and bioinformaticians. Applications include sequence alignment, database searching, protein motif identification, pattern analysis, genome codon usage, and presentation tools for publication.

EMBOSS also has an application-programming interface (API) that enables software developers to write their own applications and create workflows that automate complex tasks. The suite is included in many commercial bioinformatics systems and has emerged as a core component of several data integration and bioinformatics projects, including myGrid and EMBRACE.

The EMBOSS suite was developed from work initially done by Rice in the late 1980s on the GCG informatics package, while based at the European Molecular Biology Laboratory in Heidelberg, Germany. After moving to the Wellcome Trust Sanger Institute in Cambridge, England, Rice and Alan Bleasby began developing a new suite of open-source tools - EMBOSS - in 1996, with initial funding from the Wellcome Trust, and later the BBSRC and Medical Research Council.

Another benefit of the new BBSRC funding is helpdesk support. Bleasby said: “As well as helping researchers with limited bioinformatics expertise to make the most of EMBOSS, we will be able to provide better support and documentation to the estimated 20 percent of our users who are also software developers. We will encourage these experts to contribute their code to the project. In return, we will make their software widely available through the EMBOSS website and provide ongoing user support for it. This mechanism will help to ensure that EMBOSS evolves according to the needs of its users.”

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