Center for Biomolecular Science and Engineering University of California, Santa Cruz Robert Kuhn, PhD Center for Biomolecular Science and Engineering University.

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Presentation transcript:

Center for Biomolecular Science and Engineering University of California, Santa Cruz Robert Kuhn, PhD Center for Biomolecular Science and Engineering University of California, Santa Cruz FaceBase kick-off meeting Bethesda, MD November 16, 2009 UCSC Genome Browser

Thanks! Funding: NHGRI, NCI, NICHD, NIDCR, HHMI, QB3, SU2C Data: NCBI, Ensembl, UniProt, Baylor, WUSTL, UWash, IMIM, OMIM, numerous other contributors UCSC Browser team: – –David Haussler – PI – –Jim Kent – Browser Concept, BLAT, Team Leader, Co-PI – –Mark Diekhans, Fan Hsu, Angie Hinrichs, Kate Rosenbloom, Hiram Clawson, Rachel Harte, Galt Barber, Andy Pohl, Tim Dreszer, Larry Meyer, Mike Pheasant, Brian Raney, Melissa Cline – Engineering – –Donna Karolchik, Robert Kuhn, Ann Zweig, Kayla Smith, Brooke Rhead, Pauline Fujita, Katrina Learned – QA, Docs, Support – –Ting Wang, Jing Zhu, Steve Benz, Zach Sanborn – Cancer Browser – –Jorge Garcia, Victoria Lin, Erich Weiler, Alex Wolfe – KiloKluster, Sys- admin

Browser: interface to database software database tables browser  details  track (mapping) primary table secondary tables

Genome Browser traffic > 3 million hits / wk 80,000 distinct IPs / mo

Genome Browser 44-species conservation ucsc browsers on high-coverage assemblies FaceBase mirror

FOXE1 gene chromBand OMIM UCSC Genes SNPs Conservation

Genome Browser saving/sharing sessions save a session

Variation Resources chromosome 2q21.2 – 2q21.3 HapMap phased LD

Custom Tracks View private data in context of all other UCSC-hosted data. Intersect with public data. Save custom track data in Sessions.

Custom Tracks Show gain and loss of copies on chrom arm 2q gain loss

Genome Graphs Export Custom Track data to Genome Graphs

Genome Graphs for association studies

Visigene

zoom in on in-situs

UCSC Browser Mirrors mirror sites: Duke Cornell Medical College of Wisconsin Copenhagen Brisbane see also wikipedia for links

UCSC Browser Help mailing list + archives

UCSC Browser Training Online / Onsite training UCSC Open Helix

Variation Resources chromosome Xq26.3 dbSNP 129 Database of Genomic Variants Segmental Duplications

Sessions / Custom wiggle *just for fun user: Hiram session: moneyPolitics

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