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ParaFrap II -- Bioinformatics Workshop -- 3-8 July 2017, Montpellier FR        
  Monday Tuesday Wednesday Thursday Friday Saturday
  3 July 2017 4 July 2017 5 July 2017 6 July 2017 7 July 2017 8 July 2017
9 Overview and Introductions Genome Browser Exercises - II
(Group Exercise)
RNA-seq Mapping Exercise - II
(Group Exercise)

Functional Genomics Exercises Intro to Regular Expressions Group Project Presentations
  Bastien, Baumgarten, Harb,
MacPherson, Roos, Warrenfeltz
Analysis & interpretation of
RNA-seq evidence


GBrowse Image
Interpreting RNA-seq
mapping results

Transcriptomics, Proteomics Cameron MacPherson all students

Survey
 


Pattern recognition, colocation
 
10 Who are you?  What do you do? Roos et al Harb et al  Warrenfeltz et al
 
  Turbo-Intros by all students
1-2 slides, 2-3 min max
      Sequence analysis Exercises

Regular Expressions
More Regular Expressions
Warrenfeltz et al
 
 
      Tea / Coffee  
11 Tea / Coffee Tea / Coffee Tea / Coffee Tea / Coffee Pathway Exercises
Metabolism & Pathways
Tea / Coffee
    Results of RNA-seq analysis SNP Mapping Exercise - I

Variant calling (Galaxy)
(Group Exercise)
Host
response datasets
Metabolic Pathways
all students
    all students        Harb Warrenfeltz et al Harb et al  
12 Seminar/Discussion (over lunch) Seminar/Discussion (over lunch) Seminar/Discussion (over lunch) Seminar/Discussion (over lunch) Lunchtime Discussion  
  Designing & mining pathogen
genome databases
Genomic-scale analysis of trans-
criptional reg'n in kinetolastida
Epigenomic control in
Plasmodium
Dissecting structure / function
relationships in the kinetoplastida
Intro to complex queries, data
integration & group projects
 
 




Lunch & Farewell
13 David Roos, Univ Pennsylvania Nicolai Siegel, Univ W�rzburg Sebastian Baumgarten, Inst Pasteur Eva Gluenz, Oxford University all instructors  
  Lunchbox Lunchbox Lunchbox Lunchbox Lunchbox  
             
14 Intro to EuPathDB databases RNA-seq Mapping Exercise - I
(Group Exercise)
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Free time / Group activity? Intro to SNPs & Population
Biology
Group Projects
(Group Exercise)
 
  Omar Harb Mapping RNAseq data (Galaxy)   David Roos all students, all instructors  
  Gene Page Exercises Warrenfeltz et al   SNP mapping Exercise - II
(Group Exercise)
   
15 Finding genes, interpreting
gene pages; Intro to search
strategies

    Interpreting variant calling
results
   
 
   
   
  Warrenfeltz et al     Harb et al    
16 Tea / Coffee Tea / Coffee   Tea / Coffee Tea / Coffee  
    Intro to Phylogeny & Orthology        
    David Roos        
17 Genome Browser Exercises - I Orthology Exercises   Population Biology Exercises    
  Evidence tracks, alignments,
comparative genomics
Phyletic pattern queries   SNPs, Population genetics    
  MacPherson et al Roos et al   Roos et al    
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19 Welcome Dinner
Le Chat Perche
10 et 12 rue du College

Dinner (on your own) Dinner (on your own) Dinner (on your own) Closing Dinner / Party  
             
             
20