Schedules
 
Course Schedule:
 
 
July 8, Participants arrive
 
July 9-10, David Maddison:
 
  1. • Mesquite Introduction
  2. • Scripting, Pipelining, Interfacing with Mesquite
 
July 11-12, Sergei Pond and Spencer Muse
 
  1. • HyPhy Intro
  2. • Scripting with HyPhy
 
July 13-16, Rutger Vos & Jason Stajich (Perl); Stephen Smith & Jeff Oliver (Java): 
 
  1. • Object-oriented programming overview and intro
  2. • Sequences, Alignments, Trees
  3. • Distances, substitution rates, optimization
  4. • Harvesting data from data services, workflows
  5. • Writing a Mesquite module (Java)
  6. • CIPRES & Bio::Phylo environments (Perl)
 
July 17-18, Hilmar Lapp; Bill Piel
 
  1. • Intro to SQL
  2. • Using the DBI (Perl); using JDBC (Java)
  3. • Complex Queries & BioSQL
 
July 19, Bill Piel
 
  1. • Participants wrap up their projects/exercises
  2. • Departures to the airport occur throughout the day
 
Daily Timetable:
 
 
08:00 - 09:00. Coffee, check email
 
09:00 - 10:30. Session 1
 
10:30 - 10:45. Coffee break
 
10:45 - 12:15. Session 2
 
12:15 - 01:30. Lunch
 
01:30 - 03:00. Session 3
 
03:00 - 03:15. Coffee break
 
03:15 - 04:45. Session 4
 
04:45 - 07:00. R&R and dinner
 
07:00 - 09:00. Session 5:  
  1. • Problem sets
  2. • Student projects