The UCSC Team A professional informatics team of 30 FTEs with expertise in –genomics –work with domain experts worldwide –complex data and applications –large scale systems –7x24 availability –security and confidentiality A professional informatics team of 30 FTEs with expertise in –genomics –work with domain experts worldwide –complex data and applications –large scale systems –7x24 availability –security and confidentiality

One of the top 3 bioinformatics sites Over 2.5 millions hits per week ~1 million lines of code 2.5 Terabytes/server –100 databases, >5,000 tables (human) 1.3 Terabyte/week download One of the top 3 bioinformatics sites Over 2.5 millions hits per week ~1 million lines of code 2.5 Terabytes/server –100 databases, >5,000 tables (human) 1.3 Terabyte/week download UCSC Genome Browser (genome.ucsc.edu)

Centralized repository of data from 80 organizations and 33 groups –Nature, 6/4/07 –Genome Research, 6/07, 28 papers Many different types of data Successful pilot project expanding into full genome scale Centralized repository of data from 80 organizations and 33 groups –Nature, 6/4/07 –Genome Research, 6/07, 28 papers Many different types of data Successful pilot project expanding into full genome scale ENCODE ( ENCyclopedia Of DNA Elements)

Large scale phase III clinical trail –VaxGen U.S. and Thailand trials data 3 user views on –individual subjects –clinical measurements –HIV genomic sequences and annotation HTTPS secure website Large scale phase III clinical trail –VaxGen U.S. and Thailand trials data 3 user views on –individual subjects –clinical measurements –HIV genomic sequences and annotation HTTPS secure website HIV Vaccine Database (Funded by Gates Foundation*) * via GSID (Global Solutions of Infectious Diseases)

Locus Variants Track (PhenCode*) –132 external databases from 17 groups –34,000 variants with 100,000 attribute records –1,900 phenotypes Prostatic cancer, blood groups, Cystic fibrosis, Hemoglobinopathies, Immune deficiencies, Muscular dystrophy, Phenylketonuria, breast cancer, Rett Syndrome, Zellweger syndrome, RefSum Disease, Adrenoleukodystrophy, (on genome-test)Familial Hypertrophic Cardiomyopathy, Long QT Syndrome, …. –132 external databases from 17 groups –34,000 variants with 100,000 attribute records –1,900 phenotypes Prostatic cancer, blood groups, Cystic fibrosis, Hemoglobinopathies, Immune deficiencies, Muscular dystrophy, Phenylketonuria, breast cancer, Rett Syndrome, Zellweger syndrome, RefSum Disease, Adrenoleukodystrophy, (on genome-test)Familial Hypertrophic Cardiomyopathy, Long QT Syndrome, …. Connects genotypic and functional data from LSDBs ( L ocus- S pecific D ata B ases) * Belinda M. Giardine, Penn State University

VisiGene Image browser for in-situ and other gene-oriented pictures 124,000 images –18,000 from Paul Allen Brain Atlas –other sources Unique presentation technology –enabled by 7 millions of photo tiles Image browser for in-situ and other gene-oriented pictures 124,000 images –18,000 from Paul Allen Brain Atlas –other sources Unique presentation technology –enabled by 7 millions of photo tiles

VisiGene

UCSC at Your Service Understand your work & needs System solutions –Design –Development –Maintenance –User education & support –Project management Understand your work & needs System solutions –Design –Development –Maintenance –User education & support –Project management

UCSC Genome Browser

HIV Vaccine Database and Web Works

Medical Management Systems* Utilization Authorization –Internet based –Driven by clinical guidelines Milliman and Robertson InterQual Disease Management Utilization Authorization –Internet based –Driven by clinical guidelines Milliman and Robertson InterQual Disease Management * at previous startup companies