Robert Kuhn, PhDCenter for Biomolecular Science and EngineeringCenter for Biomolecular Science and Engineering

University of California, Santa CruzUniversity of California, Santa Cruz

FaceBase kick-off meetingFaceBase kick-off meeting

Bethesda, MDBethesda, MD

November 16, 2009November 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

softwaresoftware

database

tables

browser

details track (mapping)primary tablesecondary 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

chromBandOMIM

UCSC GenesSNPs

Conservation

Genome Browser saving/sharing sessions

save asession

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

Visigenezoom in on in-situs

UCSC Browser Mirrors

mirror sites:

DukeCornell

Medical College of WisconsinCopenhagen

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: Hiramsession: moneyPolitics