Date post: | 21-Dec-2015 |
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UK -Tomato Chromosome Four
Sarah ButcherBioinformatics Support Service Centre For BioinformaticsImperial College London
[email protected]/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