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The new VectorBase: our improved resource for invertebrate vectors

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17 diapositives · 366 Views · Jul 11, 2014

The new VectorBase: our improved resource for invertebrate vectors. Scott Emrich On behalf of VectorBase Eck Institute for Global Health University of Notre Dame. VectorBase is a Bioinformatic Resource Center ( BRC).

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  1. The new VectorBase: our improved resource for invertebrate vectors Scott Emrich On behalf of VectorBase Eck Institute for Global Health University of Notre Dame

  2. VectorBase is a Bioinformatic Resource Center (BRC) • VectorBase is a genome resource for invertebrate vectors of human pathogens • Funded by NIH-NIAID as part of a wider group of NIAID BRCs (see above) for biodefense and emerging and re-emerging infectious diseases • Re-competition starts this Fall (for up to 5 more years)

  3. VectorBase is still a collator of genome data Organism pages RawGenBank data from sequencing centers (our) Annotation Full release * * Pre-released* * *

  4. VectorBase is also: • A service providing tools for browsing and mining vector “-omics” data • A content generator: • Genome annotation (Dan Lawson, earlier talk) • “Driving Biological Projects” – two other talks • Committed to regular releases (5-6 per year) • A help desk to help our community on genome informatics and are responsible for facilitating data submission • Bob MacCallum’s talk yesterday

  5. In the end, VectorBase is a team And YOU!

  6. Why undergo the renovation? #

  7. Left side: • Welcome message • Available data • Tools andResources Right side: • Past jobs • Organisms (2) • Latest news

  8. Left side: • Community Right side: • Rotating tips • Newsletters • Upcoming meetings

  9. Path: Home page/Click on Over time all data will be organized as Related resources like above

  10. Transcripts and transcriptomes Path: Transcripts & Transcriptomes page/ Click on RNAseq icon

  11. This is the new organismpage: Collects strain, data, and relevant tools

  12. The Genome Browser is largely the same, except for the new “Variation” data, which is under development.

  13. Improved browseravailibilty via links On the description page click here:

  14. Keeping up with the changes https://www.vectorbase.org/releases

  15. Emerging genomes “Upcoming Genomes” table/page is now under constant development: Nominated ---> Selected ---> Initiated ---> DNA received Library construction ---> Sequence generation ---> Assembly Genome annotation ---> Community annotation ---> Paper writing Published/Completed.

  16. How to contact us and keep in sync? info@vectorbase.org (from you, to us) www.vectorbase.org/contact news@vectorbase.org (from us, to you) Forum Twitter Facebook RSSF Newsletter www.vectorbase.org/newsletters News www.vectorbase.org/news

  17. Acknowledgements • V Daniel Lawson Derek Wilson Gautier KoscielnyKarynMegy Martin Hammond Daniel Hughes Ewan Birney Paul Kersey • EMBL-EBI Imperial College FotisKafatos Bob MacCallumGeorge Christophides Frank Collins Nora Besansky Greg Madey Rob Bruggner Nate Konopinski EO Stinson Scott Emrich Andrew Sheehan Rory Carmichael Greg Davis Dave Campbell Ryan Butler Katie Cybulski Neil Lobo NoTre Dame New MexicO Maggie Werner-Washburne Phil Baker HaRvard Bill Gelbart Susan Russo Dave EmmertPinglei Zhou Lynn Crosby Kathy Campbell IMBB Kitsos Louis PantelisTopalis Emmanuel Dialynas, Vicky Driscou A Sequencers TIGR/JCVI WashU Broad Institute EnsEmbl VectorBase http://www.vectorbase.org