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/