UK -Tomato Chromosome Four

Sarah ButcherBioinformatics Support Service Centre For BioinformaticsImperial College London

s.butcher@ic.ac.ukwww.ic.ac.uk/bioinformaticswww.srcuk.org.uk

Project Team

Tomato ExpertiseGerard Bishop - Imperial College – *Principal Investigator*Graham Seymour - Horticulture Research International,

WellesbourneGlenn Bryan - SCRI Dundee (potato)Sequencing & AssemblyJane Rogers - Sanger InstituteAutomated AnnotationMIPSManual Annotation/Curation/Web-siteSarah Butcher - Imperial College

Bioinformatics Support Service

Central core bioinformatics facilities: hardware, software, databases, help-desk, web-site, consultation, training courses, collaborative research5 full-time bioinformaticians (+1 full-time annotator)Expertise: broad-based biological, sequence-based analyses, protein structure, microarrays, bespoke user interface & pipeline design, software developmentPerl, Java, XML, MySQL, SRS, web services (Tomcat, SOAP), looking at GRID middleware (GLOBUS, ICINI)

Compute

shared cluster resources

Shared HPC

BSS login serverweb server, interactive jobs

Sun V8808 x 750 MHz 32 GB RAM

24 x 750 MHz 36 GB RAM>133 nodes

dual Xeon Linux cluster

1-2GB RAM per node

200 node dual OpteronLinux cluster2-4GB RAM

per node

>16TB disk24TB near-line

tape

24 x 1.2 GHz>36GB RAM

Data

Sun Grid Engine Scheduler

Project

Sequence chromosome 4 euchromatin using BAC by BAC approach (Sanger)Annotate and curate output in collaboration with MIPSAdd into the SGN database (Cornell)

Focus framework & facilitate interactions within the UK user group - develop Solanaceous Research Community – UK (SRC-UK) Communicate through UK by web-site and by organising UK meetings

Timeline

120 BACs sequenced

73 BACs sequenced

Remaining BACs sequenced

Annotator 100 BACstraining/coord. manually50 BACs annotatedman. annotated

Remaining BACs manually annotated

Automated annotation pipeline running regularly

12 24 36 42