Avian Influenza Virus Genomics and Bioinformatics Workshop
August 6-11, 2007,
Hosted at Hanoi School of Public Health,
Hanoi, Viet Nam



Avian Influenza Virus Genomics & Bioinformatics Workshop Schedule - DRAFT

Last Updated: Thursday, August 16, 2007 4:41 AM (EDT, Washington DC, USA)

 
August 2007
  Sun Mon Tue Wed Thu Fri Sat
  5 6 (D01) 7 (D02) 8 (D03) 9 (D04) 10 (D05) 11 (D06)
               

All changes from the printed version will be in red.

Symposium Venue: Hanoi School of Public Health, 138 Giang Vo Street, Hanoi in the International Conference Room, 7th Floor. (Day 1 only)

Workshop Venue: Hanoi School of Public Health, 138 Giang Vo Street, Hanoi in 3rd Floor Computer Room. (Day 2-6)

General Basic schedule:

8:00-10:00 - lecture slot
10:00-10:30 - coffee break
10:30-12:00 - practical/lecture slot
12:00-13:00 - lunch
13:00-13:30 - self study
13:30-15:00 - practical/lecture slot
15:00-15:30 - coffee break
15:30-17:00 - practical/lecture slot
17:00-18:00 - review/self study

Organized by objectives/goals:

Monday # basic molecular virology and influenza virology
Tuesday # accessing current influenza literature and sequence information
Tuesday # depositing new gene and protein sequences in public databases
Wednesday # identifying viral reassortants and mutations of public health importance, (e.g. virulence factors, host specific changes, etc) by sequence analysis, focusing on what is known about avian flu.
Wednesday/Thursday # sequence alignments and other sequence handling software.
Thursday # measuring sequence divergence; building phylogenetic trees
Friday # full protein and epitope analysis
Friday # selecting evolutionary models
Saturday # group project and translational talk (putting everything together)


Day 1: Monday, August 6, 2007 - Basic Virology/Influenza Symposium (Open to the General Public) [Goal: basic molecular virology and influenza virology] Venue
08:00-08:30 Registration International Conference Room, 7th Floor
08:30-8:45 Welcome Remarks [WHO Representative (Michael Perdue), HSPH Representative, FAO Representative]
08:45-09:00 General Introduction/Information on the Course - Chuong Huynh
09:00-10:30 Lecture: General Virology - Malik Peiris
10:30-11:00 Coffee Break - [Symposium Group Picture]
11:00-12:00 Lecture: Introduction to Influenza Biology - Henry Wan
12:00-13:00 Lunch [in Canteen 1st Floor or Hotel or Surrounding restaurant]
13:00-13:30 Lecture: Influenza Diagnostics - Katarina Prosenc
13:30-14:00 Lecture: Recent laboratory work on avian influenza 2007 - Le Thi Quynh Mai
14:00-14:30

Lecture: Molecular Influenza: Influenza Vaccine - Michael Perdue

14:30-15:00 Lecture: The 1918 influenza pandemic and the virus - Henry Wan
15:00-15:30 Coffee Break
15:30-16:15 Lecture: The origin of the current H5N1 outbreaks - Henry Wan
16:15-17:00 Lecture: Summary of SE Asia H5N1 outbreaks to date - Gavin Smith
   
17:00 Welcome Drinks
  Reading Assignment  

Day 2: Tuesday, August 7, 2007 [Goal: accessing current influenza literature and sequence information AND depositing new gene and protein sequences in public databases ] Venue
08:00-08:30 Surprise Quiz Computer Room, 3rd Floor
08:30-10:00 Lecture: Overview of Bioinformatics Resources - Phillippe Le Mercier
Lecture: Influenza Protein Functions - Phillippe Le Mercier
10:00-10:30 Coffee Break - Picture Day [Workshop Participants/Instructors/Observers]
10:30-12:00 Practical: Overview of Bioinformatics Resources - Phillippe Le Mercier
12:00-13:00 Lunch
13:00-13:30 Self Study
13:30-15:00 Lecture/Practical: NCBI Entrez and Influenza Virus Resource - Yiming Bao
15:00-15:30 Coffee Break
15:30-17:00 Practical: NCBI Entrez and Influenza Virus Resource Yiming Bao
17:00 -18:00 Lecture: Principles of Pairwise- Chuong Huynh [theory]
Lecture: Multiple Sequence Alignment - Chuong Huynh (if time available)
     
  Reading Assignment  

Day 3: Wednesday, Auugust 8, 2007 [Goal: identifying viral reassortants and mutations of public health importance, (e.g. virulence factors, host specific changes, etc) by sequence analysis, focusing on what is known about avian flu.] [Goal: sequence alignments and other sequence handling software; Venue
  Quiz Computer Room, 3rd Floor
08:00-09:00 Lecture: Residue Analysis/Important Mutations for AIV - Vijay [Topics: get sequence of drug resistance and high pathogeneticity in the practical portion of this]
09:00-10:00 Lecture: Introduction to AIV Phylogenetic Analysis - Henry Wan (general concept) [Topics: parsimony, rooted and unrooted trees, internal trees; seq of different viruses, clarify clades; relevant antisense diff, impt ref taxa, incl genotyping, ML, NJ]
10:00-10:30 Coffee Break
10:30-11:00 continue ...
11:00-11:30 Lecture: Introduction to AIV Phylogenetic Analysis - Vijay (H5N1 reference taxa)
11:30-12:00 Demo: Sequence alignment in ClustalX and BioEdit - Vijay
12:00-13:00 Lunch
13:00-13:30 Self Study
13:30-15:00 Lecture: Contig Assembly with Staden Package - Vijay
Practical: Sequence alignment in ClustalX and BioEdit - Vijay [Topics: this is a demonstration: incl manual alignment, explain NA deletion, connecting peptide misalignment, explain pitfalls ... reference: Phylogenetic Handbook: Chapter 3: practice on bioedit and clustal]
15:00-15:30 Coffee Break
15:30-17:00

Practical: (continued)

17:00 -18:00 Self Study/Review
     
  Reading Assignment  

Day 4: Thursday, August 9, 2007 [Goal: measuring sequence divergence; building phylogenetic trees] Venue
08:00-09:00 Lecture: Evolutionary Models - Henry Wan Computer Room, 3rd Floor
09:00-09:30 Quiz
09:30-10:00 Participant Introduction
10:00-10:30 Coffee Break
10:30-12:00 Lecture/Demo: Measuring Sequence Divergence (homology) with MEGA3 - Vijay [Topics percent homology of virus; amount of divergence before considered antigentically distinct?; ...]
Practical/Demo: Construction and Interpretation of Phylogenetic Trees with MEGA3 (Neighbor Joining) - Vijay
12:00-13:00 Lunch
13:00-13:30 Self Study
13:30-15:00 Practical: Multiple sequence alignment and tree building with the NCBI influenza resources - Yiming Bao [NJ tree --> at ncbi]
15:00-15:30 Coffee Break
15:30-17:00

... continued

17:00 -18:00 continued .. or Self Study/Review
     
  Reading Assignment  

Day 5: Friday, August 10, 2007 [Goal: full protein and epitope analysis; selecting evolutionary models] Venue
  Quiz  
08:00-10:00 Demo/Practical: FindModel, GARLI, and Mr. Bayes - Vijay / Chuong [use the different models for the same dataset] Computer Room, 3rd Floor
10:00-10:30 Coffee Break
10:30-12:00

Group Project: Assign group project - Vijay / Chuong Huynh/ Henry Wan / Yiming Bao [Provide Asian isolate data set of influenza virus, look for neuramindase, high path determinant, change in receptor binding, drug resistance (oseltamivir and amantadine resistance) --> then provide a report that would be acceptable to WHO. A mock report will be provided to assist in preparing the report with leading questions.]

12:00-13:00 Lunch
13:00-13:30 Self Study
13:30-15:00

Demo/Review: More on molecular characterization: Alternative splicing; stop codons; choosing evolutionary models - which is best? - Vijay

15:00-15:30 Coffee Break
15:30-17:00

Group Project

17:00-18:00 Self Study/Review
     

Day 6: Saturday, August 11, 2007 - [Goal: Group Project and Traslational Talk] Venue
08:00-09:30 Lecture/Demo/Practical: AIV Epitope Analysis - Henry Wan - [using IEDB Analysis Resource] Computer Room, 3rd Floor
10:00-10:30 Coffee Break
10:30-11:00 Review and Practical Sessions (Open Questions with Instructors) - Phillippe Le Mercier -- Overview of Immunological concepts in epitope analysis
11:00-12:00 (continue ...with Group Project)
11:55 Group Picture -- WE MUST DO IT THIS MORNING!!!
12:00-13:00 Lunch
13:00-13:30 Self Study
13:30-15:00 (continue ...with Group Project)
15:00 Group Project due at: 3:00pm, Submit by email
15:00-15:30 Coffee Break
15:30-16:30 Group Project Presentation (only 5 groups)
16:30-17:00 Lecture: Reassortment and Genotyping - Henry Wan
xxxxx Workshop Evaluation (will open in a new web browser)  
17:00 Workshop Farewell Dinner (+ Presentation of Certificates) in the 2nd Floor Large Conference Room - directly below the computer lab 2nd Floor Conf

Day 7: Sunday, July 12, 2007 - Participant Departure Venue
     

 


Last updated: Thursday, August 16, 2007 4:41 (EDT, Washington DC)