Post on 19-Dec-2015
HIV Vaccine Database and Web
Works
HIV Vaccine Database and Web
Works
UCSC BidUCSC Bid
HIV Vaccine Database and Web
Works
HIV Vaccine Database and Web
Works
UCSC Status ReportUCSC Status Report
• GSID Project TeamJim Kent (lead, The Bioinformatitian)
- the man who saved the Public Genome Project
• GSID Project TeamJim Kent (lead, The Bioinformatitian)
- the man who saved the Public Genome ProjectFan Hsu (engineer, coordinator)Galt Barber (engineer)Bob Kuhn (QA)Erich Weiler (system admin)
Fan Hsu (engineer, coordinator)Galt Barber (engineer)Bob Kuhn (QA)Erich Weiler (system admin)
• genome.ucsc.edu– one of the top 3 bioinformatics sites– ~1 million lines of code– over 2.5 millions hits per week
• genome.ucsc.edu– one of the top 3 bioinformatics sites– ~1 million lines of code– over 2.5 millions hits per week
UCSC Genome Browser TeamUCSC Genome Browser Team
Project OverviewProject Overview
• Relational database encompassing all significant trial data
• Web works involving 3 primary views for accessing data
Subject ViewTable ViewSequence View
• Relational database encompassing all significant trial data
• Web works involving 3 primary views for accessing data
Subject ViewTable ViewSequence View
Subject View (proposed)Subject View (proposed)
Subject View (delivered)Subject View (delivered)
Table View (proposed)Table View (proposed)
Table View (delivered)Table View (delivered)
Table View (delivered)Table View (delivered)
Sequence View (proposed)Sequence View (proposed)
Sequence View (in progress)Sequence View (in progress)
Select Subjects (delivered)Select Subjects (delivered)
Milestone 0Milestone 0
• Signing Agreement between GSID and UCSC
Done. (11/2006) Whew!
• Signing Agreement between GSID and UCSC
Done. (11/2006) Whew!
Milestone 1Milestone 1
• VAX004 sequence and clinical data imported into MySQL database
• Prototype of homepage developed• Subscription and login pages implemented
with mock credit cards• Subject View finalized
Done. (2/10/07)
• VAX004 sequence and clinical data imported into MySQL database
• Prototype of homepage developed• Subscription and login pages implemented
with mock credit cards• Subject View finalized
Done. (2/10/07)
Milestone 1bMilestone 1b
• System maintenance* • Hardware spec*• Linux system install & configuration*• UCSC deliverables install/configuration*
• UCSC QA
• Done. (2/10/07)
• System maintenance* • Hardware spec*• Linux system install & configuration*• UCSC deliverables install/configuration*
• UCSC QA
• Done. (2/10/07)* Under separate contract to Bioinformatics
Professionals* Under separate contract to Bioinformatics
Professionals
Milestone 2Milestone 2
• Table View finalized and implemented • Real credit cards taken in subscription • Prototype Sequence View available
Done. (5/11/07)– also added Select Subjects
• Table View finalized and implemented • Real credit cards taken in subscription • Prototype Sequence View available
Done. (5/11/07)– also added Select Subjects
Milestone 3Milestone 3
• Sequence View finalized• Home page finalized • Documentation finalized• Database available for test & launch
• ETA 8/15/07
• Sequence View finalized• Home page finalized • Documentation finalized• Database available for test & launch
• ETA 8/15/07
First Year Status SummaryFirst Year Status Summary
Milestone 0- contract
Milestone 1 & 1b- Subject View
Milestone 2- Table View- Security/Registration/Payment- Select Subjects
• Milestone 3 (8/15/07)- Sequence View
Milestone 0- contract
Milestone 1 & 1b- Subject View
Milestone 2- Table View- Security/Registration/Payment- Select Subjects
• Milestone 3 (8/15/07)- Sequence View
Thank YouThank You
DemoDemo
Security/Signup/Payment(delivered)
Security/Signup/Payment(delivered)
2nd and 3rd Years2nd and 3rd Years
• 2nd Year- VAX003 data- alignment tools- proteomics tools
• 3rd Year- gp160 data- additional alignment tools- data from Keith Crandall
• 2nd Year- VAX003 data- alignment tools- proteomics tools
• 3rd Year- gp160 data- additional alignment tools- data from Keith Crandall