Award details

The GARNet Transcriptomics and Bioinformatics service III

Reference	BB/E01772X/1
Principal Investigator / Supervisor	Professor Sean May
Co-Investigators / Co-Supervisors
Institution	University of Nottingham
Department	Sch of Biosciences
Funding type	Research
Value (£)	791,919
Status	Completed
Type	Research Grant
Start date	01/04/2007
End date	31/03/2010
Duration	36 months

Abstract

This grant application requests a continuation and enhancement of NASC's bioinformatics activities as a public data warehouse and service for Arabidopsis. The GARNet programme has provided transcriptomics, phenotype and various associated bioinformatics services for the Arabidopsis community via NASC. GeneChip data from NASCarrays has been disseminated to the wider user community through an open website with no restrictions. The GARNet service has also provided the entire NASC informatics infrastructure for maintenance and development of our European seed and DNA stock data and distribution catalogue. In addition the programme has allowed us to adopt all relevant standards (MIAME, PO, PATO) and to co-operate with the appropriate bodies in transcriptomics, phenomics and distributed computing in order to build better and more useful services. We are asking for support to continue our integrated bioinformatics services under the guidance of the democratically elected Arabidopsis community advisory body / GARNet. We also wish to extend the service to include distributed access to Genespring workgroup software for GeneChip users in order to fill some of the analysis needs identified by our users.

Summary

This grant application requests a continuation and enhancement of previous work extending back for many years where NASC has acted as a public data warehouse and service for the model plant - Arabidopsis. For several years, the UK Arabidopsis community has had access to a variety of technological and informatic (database and computational) services that were provided for it by NASC under the umbrella of a multi-site consortium called GARNet. These included very large numbers (thousands) of GeneChip results that had recorded information on what all of the 22,000+ genes in a plant were doing at various times and under defined conditions. This GeneChip data from NASCarrays has been disseminated to the plant user community through an open website with no restrictions for use or location. The GARNet service also made it possible to maintain, develop and renovate the much older NASC database and user catalogue relating to seed and DNA stock data and distribution of seed stocks. In addition the programme has allowed NASC to co-operate with all of the appropriate and relevant international bodies in order to build better, more useful and more open services. As part of this, NASC has adopted the common languages (also known as ontologies and controlled vocabularies) that have been internationally defined to make interchange between widely distributed databases possible and precise. NASC is spplying for support to continue this integrated information services under the guidance of the democratically elected Arabidopsis community advisory body / GARNet. NASC also wishes to extend the service to include stronger and more user-friendly analysis tools for all users of GeneChip data on arabidopsis regardless of their location or local facilities. This last approach is in response to specific needs identified by users from the plant community.

Committee	Closed Committee - Genes & Developmental Biology (GDB)
Research Topics	Plant Science
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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