2012 EuPathDB Workshop

2012 Schedule

The course begins at 6:30 pm on Sunday, June 17th with a reception.
(If you arrive before the 4:00 pm hotel check-in time, you can call that day to see if your room is available for earlier check in. The Hotel can not guarantee your room will be ready before 4:00 pm. The number is 1-706-549-4433. There is a free hotel shuttle that can take you downtown for sightseeing while you wait.)

The course will finish at 5pm on Wednesday, June 20th.

Participants will be provided with desktop computers to use in the workshop sessions. You are welcome to bring your own laptop to use in other areas. The Holiday Inn Hotel provides free high-speed Internet in all rooms and lobby.

Quick Links: EuPathDB | AmoebaDB | CryptoDB | GiardiaDB | OrthoMCL DB | MicrosporidiaDB | PiroplasmaDB | PlasmoDB | ToxoDB | TrichDB | TriTrypDB


Date Time Place Event Instructor
Sunday, June 17th 6:30-9:00pm Holiday Inn
Georgian Ballroom
Registration & Welcome Reception -

General introduction to EuPathDB and omics


- Workshop attendees and instructors introductions
- Transportation information
Jessie Kissinger
Omar Harb
Susanne Warrenfeltz
Monday, June 18th 7:00am Holiday Inn
Redfearn Grille
Optional Breakfast (breakfast coupons provided in welcome packet)
8:30-8:45am Life Sciences
Room C128
General Workshop Introduction Eileen Kraemer
Susanne Warrenfeltz
Omar Harb
8:45-9:00am Room C128 Introductory Glossary Survey
9:00-9:45am Room C128 Site Usability Exercise Eileen Kraemer
Susanne Warrenfeltz
9:45-10:30am Room C128 Introduction to EuPathDB sites and the search strategy system Omar Harb
10:30-10:45am Room B116 Morning Coffee Break (food provided)
10:45-12:15pm Room C128

Exercise I: Finding genes and exploring gene pages

Susanne Warrenfeltz
12:15-1:15pm Room B116 Lunch (provided)
1:15-2:00pm Room C128

Exercise II: Using the genome browser

Omar Harb
2:00-2:45pm Room C128

Exercise III: RNA sequence data analysis (Part 1: using pathogen portal's RNAseq pipeline)

Omar Harb
Brian Brunk
Jessica Kissinger
2:45-3:00pm Room B116 Afternoon Snack Break (provided)
3:00-4:00pm Room C128

Exercise IV: Population (SNPs) data

Polymorphisms SNPs and Alleles

Brian Brunk
4:00-5:30pm Room C128 Sneak preview and Beta testing new features in EuPathDB:

Galaxy User Interface

Galaxy Survey

Site Search Survey

All
6:00-8:00pm Coverdell Center
Room 340
Dinner
Tuesday, June 19th 7:30am Holiday Inn
Redfearn Grille
Optional Breakfast
9:00-10:00am Life Sciences
Room C128

Exercise V: Protein motifs and domains

Regular Expression Handout

Omar Harb
10:00-10:30am Room C128

Exercise VI: DNA motifs

Brian Brunk
Susanne Warrenfeltz
10:30-10:45am Room B116 Morning Coffee Break (food provided)
10:45-11:15am Room C128 Exercise VI: DNA motifs (continued)
11:15-12:15pm Room C128

Exercise VII: Isolate data

Omar Harb
12:15-1:15pm Room B116 Lunch (provided)
1:15-2:15pm Room C128

Exercise VIII: Orthology and phylogenetic profiles

Omar Harb
2:15-2:45pm Room C128

Exercise IX: Data retrieval and download

Omar Harb
Susanne Warrenfeltz
2:45-3:00pm Room B116 Afternoon Snack Break (provided)
3:00-4:00pm Room C128

Exercise X: RNA sequence data analysis

(Part 2: viewing and analyzing your results continuation of exercise 3).
Omar Harb
4:00-5:30pm Room C128

Exercise XI: Exploring proteomics data

Short presentation: Proteomics Data at EuPathDB

Brian Brunk
Wednesday, June 20th 7:30am Holiday Inn
Redfearn Grille
Optional Breakfast
9:00-10:30am Life Sciences
Room C128

Exercise XII, Part I: Exploring transcriptomic data

Brian Brunk
Omar Harb
10:30-10:45am Room B116 Morning Coffee Break (food provided)
10:45-12:15pm Room C128 Exercise XII, Part II: Exploring transcriptomic data Brian Brunk
Omar Harb
12:15-1:15pm Room B116 Lunch (provided)
1:15-2:45pm Room C128

Exercise XIII: Complex strategy using genomic colocation

Omar Harb
2:45-3:00pm Room B116 Afternoon Snack Break (provided)
3:00-4:00pm Room C128

Exercise XIV: Complex strategy (finding vaccines and drug targets)

David Roos
4:00-4:30pm Room C128 Outreach Omar Harb
Susanne Warrenfeltz
4:30-5:00pm Room C128

Exit survey and general discussion