[EMBOSS] EMBOSS Funding News

Peter Rice pmr at ebi.ac.uk
Fri Apr 28 05:04:31 EDT 2006

EMBOSS will be funded by the UK Biotechnology and Biological Sciences 
Research Council (BBSRC) for the next 3 years. EBI has issued the 
following press release, also available from:


The EMBOSS team would like to thanks all our users and developers for 
their patience over the past two years.


Peter Rice
Alan Bleasby
Jon Ison

A brighter future for Europe’s favourite molecular biology software package

New funding for EMBOSS – Europe’s leading suite of molecular biology 
analysis tools – guarantees open access for researchers and software 

Hinxton, 25 April, 2006 – EMBOSS, the European Molecular Biology Open 
Software Suite, has received a vital funding boost from the UK 
Biotechnology and Biological Sciences Research Council (BBSRC) that will 
guarantee its continued maintenance under an open source license for the 
next three years. This ends two years of uncertainty over the future of 
the project.

Until recently, EMBOSS was hosted by the Medical Research Council’s 
Rosalind Franklin Centre for Genomics Research (RFCGR), where it was 
funded jointly by the BBSRC and the Medical Research Council (see ‘notes 
for editors’ for more information on the history of EMBOSS). With the 
announcement in April 2004 of the RFCGR’s closure, the future of EMBOSS 
hung in the balance. The new funding from the BBSRC means that EMBOSS 
co-founders Peter Rice and Alan Bleasby will be able to continue the 
EMBOSS project at the EMBL-EBI for the next three years. EMBOSS will 
remain freely available from emboss.sourceforge.net and anyone who wants 
to develop it further will have access to its source code. ‘We’re 
delighted that the BBSRC has recognized EMBOSS as an important tool for 
molecular biology’ says project leader Peter Rice. ‘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 provides a powerful package of around 300 applications for 
molecular biology and bioinformatics analysis. Molecular biologists use 
EMBOSS at all stages of their research, from planning experiments to 
analysing results. It also has an application-programming interface 
(API) that enables software developers to write their own EMBOSS 
applications. These can readily be strung together, allowing users to 
create ‘workflows’ that automate complex and time-consuming tasks. 
EMBOSS has also been used in many commercial software developments and 
is included in commercial bioinformatics systems. Its flexibility has 
made it an obvious core component of several data integration and 
bioinformatics infrastructure projects, including myGrid and EMBRACE.

The new funding also provides helpdesk support for EMBOSS’s users. ‘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% of our users who are also software 
developers’, explains Alan Bleasby. ‘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.’


Cath Brooksbank PhD, EMBL-EBI Scientific Outreach Officer, Hinxton, UK, 
Tel: +44 1223 492 552, www.ebi.ac.uk, cath at ebi.ac.uk
Anna-Lynn Wegener, EMBL Press Officer, Heidelberg, Germany, Tel: +49 
6221 387 452, www.embl.org, wegener at embl.de

Notes for editors – a brief history of EMBOSS

EMBOSS, an open source suite of tools for the analysis of biological 
data, has its origins in the late 1980s when Peter Rice, a co-founder of 
EMBOSS, was working at EMBL. Encouraged by his colleagues in the lab, he 
began to write extensions to the GCG package, which at that time 
provided its source code to users. His efforts evolved into EGCG 
(extended GCG) and Rice moved to the Sanger Centre (now the Wellcome 
Trust Sanger Institute) to continue its development. However, the 
changes to the source code licensing of GCG in 1996 put an end to 
further development of EGCG. Recognizing the importance of free source 
code to the rapid and cost-effective development of bioinformatics 
tools, Rice, in collaboration with Alan Bleasby (then at SEQNET, 
Daresbury, UK) began working on a new suite of open-source 
bioinformatics tools – the EMBOSS project – in 1996. EMBOSS has been 
funded by: the Wellcome Trust (1997–2000); the BBSRC and MRC 
(2001–2004); and through two posts at the MRC Rosalind Franklin Centre 
for Genomic Research following a merger with BBSRC’s SEQNET facility in 
1998.After the closure of RFCGR in July 2005,EMBOSS moved to the 
EMBL-EBI where it is coordinated by Rice and Bleasby.

About EMBL:

The European Molecular Biology Laboratory is a basic research institute 
funded by public research monies from 19 member states (Austria, 
Belgium, Croatia,Denmark, Finland, France,Germany,Greece, Iceland, 
Ireland, Israel, Italy, the Netherlands,Norway, Portugal, Spain, Sweden, 
Switzerland and the United Kingdom). Research at EMBL is conducted by 
approximately 80 independent groups covering the spectrum of molecular 
biology. The Laboratory has five units: the main Laboratory in 
Heidelberg, and Outstations in Hinxton (the European Bioinformatics 
Institute), Grenoble, Hamburg, and Monterotondo near Rome. The 
cornerstones of EMBL’s mission are: to perform basic research in 
molecular biology; to train scientists, students and visitors at all 
levels; to offer vital services to scientists in the member states; to 
develop new instruments and methods in the life sciences and to actively 
engage in technology transfer activities. EMBL’s International PhD 
Programme has a student body of about 170. The Laboratory also sponsors 
an active Science and Society programme.Visitors from the press and 
public are welcome.

About EBI:

The European Bioinformatics Institute (EBI) is part of the European 
Molecular Biology Laboratory (EMBL) and is located on the Wellcome Trust 
Genome Campus in Hinxton near Cambridge (UK). The EBI grew out of EMBL's 
pioneering work in providing public biological databases to the research 
community. It hosts some of the world's most important collections of 
biological data, including DNA sequences (EMBL-Bank), protein sequences 
(UniProt), animal genomes (Ensembl), three-dimensional structures (the 
Macromolecular Structure Database), data from microarray experiments 
(ArrayExpress), protein–protein interactions (IntAct) and pathway 
information (Reactome).The EBI hosts several research groups and its 
scientists continually develop new tools for the biocomputing community.

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