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