HIV Vaccine Database and Web Works UCSC Bid

HIV Vaccine Database and Web Works UCSC Status Report

GSID Project Team Jim Kent (lead, The Bioinformatitian) - the man who saved the Public Genome Project GSID Project Team Jim Kent (lead, The Bioinformatitian) - the man who saved the Public Genome Project Fan 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 Team

Project Overview Relational database encompassing all significant trial data Web works involving 3 primary views for accessing data Subject View Table View Sequence View Relational database encompassing all significant trial data Web works involving 3 primary views for accessing data Subject View Table View Sequence View

Subject View (proposed)

Subject View (delivered)

Table View (proposed)

Table View (delivered)

Sequence View (proposed)

Sequence View (in progress)

Select Subjects (delivered)

Milestone 0 Signing Agreement between GSID and UCSC Done. (11/2006) Whew ! Signing Agreement between GSID and UCSC Done. (11/2006) Whew !

Milestone 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 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

Milestone 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 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 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 You

Demo

Security/Signup/Payment (delivered)

2 nd and 3 rd Years 2 nd Year -VAX003 data -alignment tools -proteomics tools 3 rd Year -gp160 data -additional alignment tools -data from Keith Crandall 2 nd Year -VAX003 data -alignment tools -proteomics tools 3 rd Year -gp160 data -additional alignment tools -data from Keith Crandall