The Environmental Genomics Thematic Programme Data Centre Dawn

The Environmental Genomics Thematic Programme Data Centre Dawn Field, Director Dawn Field

Dawn Field dfield@ceh. ac. uk The Environmental Genomics Thematic Programme l l l Funded by the NERC at £ 16. 5 m Aimed at understanding the molecular basis of evolutionary change, organismal phenotype, and ecosystem function Evolutionary and Ecological theory plus Genomic technologies Round 1 (17) funded in Sept, 2001, Round 2 to be funded in April 2003 Data Centre to be Launched October 2002 for a period of 5 years

Dawn Field dfield@ceh. ac. uk The Environmental Genomics Thematic Programme FOR MORE INFO. . . Programme http: //www. nerc. ac. uk/funding/thematics/envgen/ Data Centre http: //envgen. nox. ac. uk/

Dawn Field dfield@ceh. ac. uk Data Management

Dawn Field dfield@ceh. ac. uk The Environmental Genomics Thematic Programme l Data • • to be generated 25 -30 Awardees producing genomic data non-model organisms microbes to vertebrates key area of overlap in data is microarray and EST data

Dawn Field dfield@ceh. ac. uk The Data Initiative Must comply with NERC data policy, balanced by science driven Awardee requirements: l l l Heterogeneity and complexity of genomic data Emerging standards, especially for microarray data (MIAME, MAGE-ML) and beyond that proteomics and metabolomics) Importance of meta-data collection Emphasis on need for Local solutions Emphasis on need for bioinformatics training and skill development

Dawn Field dfield@ceh. ac. uk The Goals of the Data Centre The CEH Oxford EG Thematic programme Data Centre will provide the data warehouse for the Programme according to the requirements of the NERC Policy for data management. Working with Bioinformatics Partners to provide and develop specific file formats, analysis tools, and data archiving methods will allow the use of common software solutions that will maximise the value of the final data holding.

Dawn Field dfield@ceh. ac. uk Data Centre - Mission The mission of the EG Data Centre at CEH Oxford is to assure that: • All Awardees have the means to collect and submit their data to the Centre • We create the capacity and expertise within the Centre to collect, manage, distribute, protect, and exploit the collective data holdings • All EG generated genomic data is eventually accessible long-term by the wider-community in an organised and add-value format • We create the opportunity for affordable 'buy-in' options for future Research council-funded science initiatives • Scale to meet future demand

Dawn Field dfield@ceh. ac. uk Data Centre - Mission We will implement this mission through the creation of: • A Data Centre Team with expertise in bioinformatics, database management, and computing • A computing infrastructure (hardware and software) that will include both centralised resources and a network of specialised computers in Awardee Labs

Dawn Field dfield@ceh. ac. uk Integration & Implementation

Dawn Field dfield@ceh. ac. uk Bioinformatics Partnerships FOR MORE INFO. . . l Silicon Genetics • http: //www. silicongenetics. com/cgi/Si. G. cgi/index. smf l max. D • http: //bioinf. man. ac. uk/microarray/resources. html l Nembase • http: //nema. cap. ed. ac. uk/nematode. ESTs/nembase. html l The Centre • http: //envgen. nox. ac. uk/

Dawn Field dfield@ceh. ac. uk Centre Overview l Bioinformatics Software Solutions • Gene. Spring/Ge. Net/Script. Editor • max. D (meta-data policies) • Partial Genome Sequence Analysis Pipeline and Database System • Bio-Red. Hat 7. 3 (Custom Designed Linux Distribution for Bioinformatics Research that will include Gene. Spring, Edinburgh's Partial Genome Sequence Tools, and max. D), • Bioinformatics for the PC Toolkit (Unix Emulation for tools in Bio-Red. Hat 7. 3)

Dawn Field dfield@ceh. ac. uk Centre Overview l Location • CEH Oxford (MAN, EDIN) l Centre Team • Bioinformatician, Data Manager, Linux Developer, Technical Administrator • 4 Developers (MAN, EDIN) l Computational Infrastructure • Commodity Hardware running Linux, combination of open source and commercial software

Dawn Field dfield@ceh. ac. uk Centre Overview l Community Development • Web site, Mailing Discussion Boards, Workshops l Teaching Lists, Help Desk(s), Presentations at EG and Training • EGDC Documentation Project, Bio-Red. Hat Workshops, Bioinformatics Training in the context of supported software and access to total data holdings, 8 EPSRC/BBSRC MRes /DPhil placements

Dawn Field dfield@ceh. ac. uk Centre Overview l Data Holdings • microarray data repository (Ge. Net) • EST sequence warehouse l Bio-IT and Knowledge-based Tangibles • Bio-Linux • Extensive Documentation Archive (FAQ, Links, Installation and usage documents) • Data Centre “Toolkit”

Dawn Field dfield@ceh. ac. uk Centre Overview: Future Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Centre Overview: Sept 2002 Bio-Linux Centre Bio-PC recipes www Software HELP files Funded labs Help Desk Ge. Net microarray repository

Dawn Field dfield@ceh. ac. uk Centre Overview: Oct 2002 Bio-Linux Centre Help Desk Ge. Net microarray repository Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software

Dawn Field dfield@ceh. ac. uk Centre Overview: winter Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Centre Overview: April 2003 Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Centre Overview: Aug 2003 Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Centre Overview: Future Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Centre Overview: Future Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Centre Overview: Future Bio-Linux Centre Help Desk Ge. Net microarray repository EST sequence warehouse Bio-PC recipes Software HELP files Funded labs Gene. Spring microarray analysis software EST pipeline

Dawn Field dfield@ceh. ac. uk Summary New Thematic, New Centre l Efforts are focused on solutions that take advantage of existing UK Bioinformatics projects, provide scalability, open access, and aim to produce added value data sets l expertise, tools, data holdings for environmental genomics researchers l Dawn Field, Director of Centre: dfield@ceh. ac. uk Jason Snape, Science Co-ordinator: jason. snape@brixham. astrazeneca. com Fiona C. Knight, Programme Co-ordinator: fclk@nerc. ac. uk http: //envgen. nox. ac. uk/