HIV Sequence & Immunology Database Workshops

HIV Sequence & Immunology Database Workshops

Meeting
Venue: 
Nelson R. Mandela School of Medicine
Event Date & Time: 
Monday, 9 September, 2019 - 08:30 to 15:30

Almost any HIV researcher has a lot to gain from learning more about HIV databases and tools. DO NOT miss this opportunity to attend these SANTHE training workshops on the HIV Sequence Database and Tools and the Immunology Database and Tools.

 

WORKSHOP INSTRUCTOR:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Dr Brian Foley, HIV Databases at LANL

Dr Brian Foley has worked in bioinformatics since 1984 - 1989 when he worked for GenBank. He then earned his PhD from the University of Vermont in molecular genetics (1995).  He is currently a research scientist at the Los Alamos National Laboratory (LANL) in New Mexico, where he works on the HIV Genetic Sequences and Immunology Databases.  He also has a contract with the Statistical and Data Analysis Center (SDAC) of the AIDS Clinical Trials Group (ACTG) at Harvard, to assist with data analysis of HIV sequences for pediatric and adult AIDS clinical trials.  Dr Foley is keenly interested in evolution and epidemiology, and has applied his interests to other pathogens such as Zika virus, Ebola virus, and Clostridium botulinum bacterial genomics.  

 

In addition to the workshops on Monday, Dr Foley will be available to meet with any interested researchers on Tuesday.  BOOK HERE for appointments (first come first served).

 

ELIGIBILITY AND WORKSHOP REQUIREMENTS:

  • People affiliated to SANTHE, AHRI, HPP, UKZN, KRISP and CAPRISA may attend one or both workshops. PLEASE REGISTER YOUR INTEREST HERE.
  • Bring a laptop computer with internet access (venue has free WiFi).
  • Teas and lunch will be provided and although vegetarian options will be available, special dietry requirements will not be catered for.

 

WORKSHOP CONTENT:

Workshop 1 : HIV Sequence Database         

Dr Brian Foley will give a talk and hands-on workshop of the uses of the HIV Genetic Sequences Database and tools at LANL (http://hiv.lanl.gov).  The HIV Sequence Database at LANL is used by researchers all over the world, for the study of HIV and other viruses.  Although the sequences in our database are HIV (and other primate lentiviruses), tools at the HIV databases can be used for the study of any organism.  For the workshop, participants should ideally bring a laptop computer with internet access (web browser such as Firefox).  Dr Foley will lead the participants through many examples of how to download data from our databases, combine it with their own data.  The sequence database workshop focuses on the virus genes, including demonstration of the use of phylogenetic methods available through the HIV Sequence Database data analysis tools menu:

 

Workshop 2 : HIV Immunology Database    

Dr Brian Foley will give a talk and hands-on workshop on the uses of the LANL HIV Immunology Database. The immunology database is integrated with the sequence database so that T-cell and B-cell antigenic regions can be studied from perspective sequence variability, and the relative location of epitopes in proteins mapped, and studies cross-compared. Summaries of what is known about an epitope or antibody and literature links are available. Basic sequence analysis and immunological computational tools, designed specifically to aid HIV researchers but often with more general applications, have been developed at the database and are widely used.  Rapid advances in sequencing and immunological method technologies have made database/computational facilitates an increasingly important aspect of pathogen/host studies. Recent renewed interest in broadly neutralizing antibodies has led to the development of now tools such as CATNAP (Compile, Analyze and Tally NAb Panels); https://www.hiv.lanl.gov/components/sequence/HIV/neutralization/index.html and CombiNAber (A tool for Prediction & Analysis of Neutralization by Antibody Combinations); https://www.hiv.lanl.gov/content/sequence/COMBINABER/combinaber.html

 

WORKSHOP FORMAT:

Workshop 1: HIV Sequence Database

08.30am - workshop starts

10.20am - tea/coffee break

10.30am - workshop resumes

12.00pm - lunch break

Workshop 2: HIV Immunology Database

01.00pm - workshop starts

03.00pm - tea/coffee break

03.20pm - workshop resumes

04.30pm - workshop ends