UK -Tomato Chromosome Four Sarah Butcher Bioinformatics Support Service Centre For Bioinformatics Imperial College London

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Presentation transcript:

UK -Tomato Chromosome Four Sarah Butcher Bioinformatics Support Service Centre For Bioinformatics Imperial College London

Project Team Tomato Expertise Gerard Bishop - Imperial College – *Principal Investigator* Graham Seymour - Horticulture Research International, Wellesbourne Glenn Bryan - SCRI Dundee (potato) Sequencing & Assembly Jane Rogers - Sanger Institute Automated Annotation MIPS Manual Annotation/Curation/Web-site Sarah Butcher - Imperial College

Bioinformatics Support Service Central core bioinformatics facilities: hardware, software, databases, help-desk, web-site, consultation, training courses, collaborative research 5 full-time bioinformaticians (+1 full-time annotator) Expertise: broad-based biological, sequence-based analyses, protein structure, microarrays, bespoke user interface & pipeline design, software development Perl, Java, XML, MySQL, SRS, web services (Tomcat, SOAP), looking at GRID middleware (GLOBUS, ICINI)

Compute shared cluster resources Shared HPC BSS login server web server, interactive jobs Sun V880 8 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 Opteron Linux cluster 2-4GB RAM per node >16TB disk 24TB 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 MIPS Add 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 BACs training/coord. manually 50 BACs annotated man. annotated Remaining BACs manually annotated Automated annotation pipeline running regularly