the environmental genomics thematic programme data centre
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The Environmental Genomics The Environmental Genomics Thematic Programme Data Thematic Programme Data CentreCentre
Dawn Field, Director
Dawn Fielddfield@ceh.ac.uk
The Environmental Genomics The Environmental Genomics Thematic ProgrammeThematic Programme Funded by the NERC at £16.5m 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 Fielddfield@ceh.ac.uk
The Environmental Genomics The Environmental Genomics Thematic ProgrammeThematic Programme
Programmehttp://www.nerc.ac.uk/funding/thematics/envgen/
Data Centrehttp://envgen.nox.ac.uk/
FOR MORE INFO...
Dawn Fielddfield@ceh.ac.uk
Data ManagementData Management
Dawn Fielddfield@ceh.ac.uk
The Environmental Genomics The Environmental Genomics Thematic ProgrammeThematic ProgrammeData 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 Fielddfield@ceh.ac.uk
The Data InitiativeThe Data Initiative
Must comply with NERC data policy,
balanced by science driven Awardee
requirements: 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 Fielddfield@ceh.ac.uk
The Goals of the Data CentreThe 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 Fielddfield@ceh.ac.uk
Data Centre - MissionData Centre - Mission
The mission of the EG Data Centre at CEH Oxford is to assurethat:
• 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 Fielddfield@ceh.ac.uk
Data Centre - MissionData 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 Fielddfield@ceh.ac.uk
IntegrationIntegration& &
ImplementationImplementation
Dawn Fielddfield@ceh.ac.uk
Bioinformatics PartnershipsBioinformatics Partnerships
Silicon Genetics• http://www.silicongenetics.com/cgi/SiG.cgi/index.smf
maxD• http://bioinf.man.ac.uk/microarray/resources.html
Nembase• http://nema.cap.ed.ac.uk/nematodeESTs/nembase.html
The Centre• http://envgen.nox.ac.uk/
FOR MORE INFO...
Dawn Fielddfield@ceh.ac.uk
Centre OverviewCentre Overview
Bioinformatics Software Solutions• GeneSpring/GeNet/ScriptEditor• maxD (meta-data policies)• Partial Genome Sequence Analysis Pipeline
and Database System• Bio-RedHat 7.3 (Custom Designed Linux
Distribution for Bioinformatics Research that will include GeneSpring, Edinburgh's Partial Genome Sequence Tools, and maxD),
• Bioinformatics for the PC Toolkit (Unix Emulation for tools in Bio-RedHat 7.3)
Dawn Fielddfield@ceh.ac.uk
Centre OverviewCentre Overview
Location• CEH Oxford (MAN, EDIN)
Centre Team• Bioinformatician, Data Manager, Linux
Developer, Technical Administrator
• 4 Developers (MAN, EDIN)
Computational Infrastructure • Commodity Hardware running Linux,
combination of open source and commercial software
Dawn Fielddfield@ceh.ac.uk
Centre OverviewCentre Overview
Community Development• Web site, Mailing Lists, Help Desk(s), Discussion
Boards, Presentations at EG Workshops
Teaching and Training• EGDC Documentation Project, Bio-RedHat
Workshops, Bioinformatics Training in the context of supported software and access to total data holdings, 8 EPSRC/BBSRC MRes /DPhil placements
Dawn Fielddfield@ceh.ac.uk
Centre OverviewCentre Overview
Data Holdings• microarray data repository (GeNet)• EST sequence warehouse
Bio-IT and Knowledge-based Tangibles
• Bio-Linux• Extensive Documentation Archive (FAQ, Links,
Installation and usage documents)• Data Centre “Toolkit”
Dawn Fielddfield@ceh.ac.uk
Centre Overview: FutureCentre Overview: Future
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: Sept 2002Centre Overview: Sept 2002
Centre
Funded labs
Bio-Linux
Bio-PCrecipes
www
GeNet microarray repository
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: Oct 2002Centre Overview: Oct 2002
Centre
Funded labs
GeNet microarray repository
GeneSpring microarrayanalysis software
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: winterCentre Overview: winter
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: April 2003Centre Overview: April 2003
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: Aug 2003Centre Overview: Aug 2003
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: FutureCentre Overview: Future
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: FutureCentre Overview: Future
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
Centre Overview: FutureCentre Overview: Future
Centre
Funded labs
GeNet microarray repositoryEST sequence warehouse
GeneSpring microarrayanalysis softwareEST pipeline
Bio-Linux
Bio-PCrecipes
Software HELP files
HelpDesk
Dawn Fielddfield@ceh.ac.uk
SummarySummary
New Thematic, New Centre 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
expertise, tools, data holdings for environmental genomics researchers
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/
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