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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
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
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
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