2014 EuPathDB Workshop

2014 Schedule

The course begins at 6:30 pm on Sunday, June 15th 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 5:00 pm on Wednesday, June 18th.

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


Time Place Event Instructor
Sunday, June 15th
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 16th
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 Introductory Glossary Survey Jessica Kissinger
9:00-9:45am

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 building search strategies

Susanne Warrenfeltz
12:15-1:15pm Room B116 Lunch (provided)
1:15-1:30pm Room C128

Glossary Survey Results

Jessica Kissinger
1:30-2:30pm

Exercise II: Viewing data on gene pages and in the Genome Browser

Susanne Warrenfeltz
2:30-2:45pm

Introduction to High throughput sequence analysis

Borodina, et al

Levin, et al

Zhang, et al

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

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

Omar Harb,
Brian Brunk
3:45-4:45pm

Introduction to SNPs in EuPathDB

Exercise IV: Population (SNPs) data

Brian Brunk
4:45-5:30pm

Exercise V: Metabolic Pathways and Compounds

Omar Harb
6:00-8:00pm Coverdell Center
Room 340
Dinner
Tuesday, June 17th
7:30am Holiday Inn
Redfearn Grille
Optional Breakfast
9:00-10:00am Life Sciences
Room C128

Exercise VI: Protein motifs and domains

RegEx Help

RegEx Lecture

Omar Harb
10:00-10:30am

Exercise VII: DNA motifs

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

Exercise VIII: Isolate data

Jessica Kissinger
12:15-1:15pm Room B116 Lunch
1:15-2:15pm Room C128

Exercise IX: Orthology and phylogenetic profiles

Brian Brunk
2:15-2:45pm

Exercise X: Data retrieval and download

Susanne Warrenfeltz
2:45-3:00pm Room B116 Afternoon Snack Break
3:00-4:00pm Room C128

Exercise XI: RNA sequence data analysis (Part 2: viewing and analyzing your results - continuation of exercise 3). Group Exercise

Omar Harb,
4:00-5:30pm Room C128

Exercise XII: Exploring proteomics data

Brian Brunk,
Susanne Warrenfeltz
5:30-5:45pm Description of Exercise XV Group Exercise Omar Harb
Wednesday, June 18th
7:30am Holiday Inn
Redfearn Grille
Optional Breakfast
9:00-10:30am Life Sciences
Room C128

Exercise XIII, Part I: Exploring transcriptomic data

Brian Brunk,
Omar Harb,
Susanne Warrenfeltz
10:30-10:45am Room B116 Morning Coffee Break
10:45-11:45pm Room C128 Exercise XIII, Part II: Exploring transcriptomic data Brian Brunk,
Omar Harb,
Susanne Warrenfeltz
11:45-12:15pm User Feedback (new features in EuPathDB)

New Features Exercise

Eileen Kraemer,
Susanne Warrenfeltz
12:15-1:15pm Room B116 Lunch
1:15-2:15pm

Exercise XIV: Complex strategy using genomic colocation

Omar Harb,
Susanne Warrenfeltz
2:15-2:45 Room C128 Designing a vaccine Omar Harb
2:45-3:00pm Room B116 Afternoon Snack Break
3:00-4:45pm Room C128

Exercise XV: Complex strategy (finding vaccines and drug targets) Group Exercise

Omar Harb
4:45-5:00pm Outreach Omar Harb,
Susanne Warrenfeltz
5:00-5:30pm Exit survey and general discussion