Los Alamos HIV Sequence, Immunology and Vaccine Trials Databases
Hands-On Workshops: Wed April 14th and Thursday April 15th.

These two workshops will be hands-on, interactive short courses, providing an introduction to some of the search and analysis tools the HIV databases provide. Participants will explore ways the database tools can facilitate a study by working through a hypothetical research problem. The faculty will answer questions about how the database might be usefully applied to the work of those attending the workshop. The courses will include a series of short presentations that will introduce several database tools. Attendees will each have a computer terminal available, and there will be time for working through example problems and queries. A syllabus will be distributed on site to workshop participants.

www.hiv.lanl.gov/ HIV Databases home page
www.hiv.lanl.gov/content/hiv-db/HIVWORKSHOP/ Syllabus and tutorial files for the workshop as it was presented (as a 3-hour single session) at the 11th CROI in San Francisco. The Whistler/Keystone workshop is nearly the same but split into two sessions.


Wednesday April 14th 12:30 - 2:00 PM

Introduction - 10 min
Sequence Database:

  ·Brian Foley - 30 min
  • Basic sequence search interface and on-the-fly alignments
  • Geography search interface
  • GeneCutter - processing nucleotide sequences
  • N-glycosite - infer N-linked glycosylation (if time permits)
  ·Bette Korber - 30 min
  • HIV database alignments and subtype reference sequences
  • Comparing "new" sequences with our reference sequences
  • Build a simple neighbor joining tree through the web
  • Using the new RIP tool for recombination analysis
  ·Brian Foley - 10 min
  • 3D views of HIV macromolecular structures

Thursday April 15th 12:30 - 2:00 PM

Introduction and Overview of Sequence Database - 10 min
Immunology Database:

  ·Bette Korber - 30 min
  • HIV/SIV sequence locator tool
  • CTL search page
  • Ab search page
  • Epitope maps
  ·Bette Korber - 30 min
  • Peptgen - list peptides for reagent development
  • Motifscan - find HLA anchor residues in a protein sequence
  • ELF - epitope location finder
Vaccine Trials Database:

  ·Brian Foley - 15 min
  • SHIV maps
  • SIV alignments
  • Vaccine database searches


NOTE: These workshops are in the Mt. Currie North Room in Delta Whistler Resort, NOT in the Conference Centre. The Delta Whistler Resort is a short walk from the Conference Centre...click here for a map.