Award details

EMBOSS: European Molecular Biology Open Software Suite

Reference	BB/D018358/1
Principal Investigator / Supervisor	Mr Peter Rice
Co-Investigators / Co-Supervisors
Institution	EMBL - European Bioinformatics Institute
Department	Rice Group
Funding type	Research
Value (£)	444,801
Status	Completed
Type	Research Grant
Start date	01/05/2006
End date	30/04/2009
Duration	36 months

Abstract

EMBOSS is an established open source bioinformatics package with about 300 applications. It has been installed at over 20,000 sites worldwide. EMBOSS development was moved to in August 2005 to the European Bioinformatics Institute with interim funding from BBSRC and MRC. This proposal will provide support for EMBOSS coordinator Dr Alan Bleasby and 2 developers who will be based at the European Bioinformatics Institute (EBI) in Hinxton. Peter Rice at EBI will continue to devote 50% of his time to the EMBOSS project as joint coordinator. EMBOSS conducted a user survey in 2004 to collect opinions on future funding and the future direction of the project, with over 1100 replies received. The vast majority (90%) favoured public funding through the research councils. This proposal will support the core development team at EBI. Core development activities will include improvements and support for the Jemboss interface, and support for other interfaces as required by specific user groups. EMBOSS is also a focus for e-Science with webservice and grid projects, including myGrid, using EMBOSS for their core analysis. This proposal will provide the ontology, metadata and provenance required by these projects. EMBOSS code is available under open source licence. Releases go through quality assurance checks that include code standards and user documentation. A core aim of this proposal is to provide high quality software and support to the UK and wider community. In the coming 5 years we will expand EMBOSS into other key areas of bioinformatics, especially protein structure, phylogenetics, gene expression, biostatistics, small molecules, proteomics and genetics. To achieve a critical mass of applications, we will be actively encouraging developers in academia and industry to contribute through training and documentation efforts. EMBOSS will use existing and new collaborations to work with other software and data integration projects in the UK, Europe and internationally.

Summary

This application is for continued core support and further development of the EMBOSS project. EMBOSS (European Molecular Biology Open Software Suite) was started in 1996 by two bioinformatics developers (Rice and Bleasby) who have developed a set of over 200 applications for the analysis of DNA and protein sequences. It is 'Open Source' software - the source code is made available to anyone who can change or extend it to meet their own needs. Users in industry have found that EMBOSS makes their life easier compared to expensive commercial packages. The funding requested will support enough programmers to maintain the core of EMBOSS for 5 years, with many new features and new applications, and will provide the basis for expanding EMBOSS further in protein structure analysis and phylogenetics and advancing into new application areas such as gene expression, proteomics, biostatistics, chemistry and genetics. As the number of applications grows, and as the user base expands, we will need to work extensively on user interfaces and other ways to make it easier for users to find and use the programs they need. All this will be made available for free, and supported by rapid response to email and telephone requests, and by training courses, online tutorials, and documentation. EMBOSS has been installed by more than 20,000 sites worldwide, many of them in the UK. A survey of users (2004) indicated the need for more support for local installations of EMBOSS and the biological databases it uses, improvements to the Jemboss program, and new ways to pass data into programs and to return results so that we can better support use of EMBOSS to build long and complex 'workflows' for routine analysis tasks. EBI will provide rapid support through the external services team in Hinxton, with the developers providing fixes for bugs, and adding requested features to future releases.

Committee	Closed Committee - Engineering & Biological Systems (EBS)
Research Topics	Structural Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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