The UCSC TeamThe UCSC Team

A professional informatics team of30 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 of30 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)

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)

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*)

HIV Vaccine Database(Funded by Gates Foundation*)

* via GSID (Global Solutions of Infectious Diseases)* via GSID (Global Solutions of Infectious Diseases)

Locus Variants Track (PhenCode*)

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 (Locus-Specific Data

Bases)

* Belinda M. Giardine, Penn State University* Belinda M. Giardine, Penn State University

VisiGeneVisiGene

• 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

VisiGeneVisiGene

UCSC at Your ServiceUCSC 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 BrowserUCSC Genome Browser

                                                          

                                                                    

HIV Vaccine Database and Web

Works

HIV Vaccine Database and Web

Works

Medical Management Systems*

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

* at previous startup companies