2015 Schedule

The course begins at 6:30 pm on Sunday, May 31st with a reception. The course will finish at 5:00 pm on Wednesday, June 3rd.

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 | FungiDB | GiardiaDB | HostDB | OrthoMCL DB | MicrosporidiaDB | PiroplasmaDB | PlasmoDB | ToxoDB | TrichDB | TriTrypDB

Instructors: Brian Brunk, Omar Harb, Jessica Kissinger, David Roos, Susanne Warrenfeltz

Time Place Event Instructor
Sunday, May 31, 2015
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
David Roos
Monday, June 1, 2015
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 Susanne Warrenfeltz, Omar Harb
Introductory Glossary Survey Jessie Kissinger
Site Usability Exercise Susanne Warrenfeltz
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

Introductory Survey Results Summary

Jessica Kissinger

Exercise II: The Genome Browser: alignments and comparative genomics

Susanne Warrenfeltz
2:30-2:45pm Room B116 Coffee Break
2:45-4:30pm Room C128 Exercise III: Interpreting RNAseq data
High resolution gbrowse image
David Roos
Exercise IV: RNA sequence data analysis (Part 1: using pathogen portal's RNAseq pipeline) Group Exercise Omar Harb


Exercise V: Data retrieval and download Brian Brunk
6:00-8:00pm Coverdell Center
Room 340
Tuesday, June 2, 2015
7:00am Holiday Inn Redfearn Grille Optional Breakfast
9:00-9:30am Room C128 Introduction to SNPs in EuPathDB Brian Brunk
Exercise VI: Population (SNPs) data Brian Brunk
Exercise VII: Protein motifs and domains
Quick-Start: Regex Cheat Sheet
Links to Regular Expression Resources
Even more Regular Expression Help
Omar Harb
12:00-1:00pm Room B116 Lunch (provided)
1:00-2:00pm Room C128

Exercise VIII: DNA motifs and genomic colocation

Susanne Warrenfeltz
Exercise IX: Orthology and phylogenetic profiles
Omar Harb
3:00-3:15pm Room B116 Coffee Break
3:15-5:15pm Room C128 Exercise X: RNA sequence data analysis (Part 2: viewing and analyzing your results - continuation of exercise 4). Group Exercise

Galaxy Project
iPlant Collaborative
Omar Harb
Exercise XI: Isolate data Jessica Kissinger
Wednesday, June 3, 2015
7:00am Holiday Inn Redfearn Grille Optional Breakfast
9:00-9:45am Room C128 Exercise XII: Metabolic Pathways and Compounds
David Roos
Exercise XIII: Exploring proteomics data
Susanne Warrenfeltz
Exercise XIV, Part 1: Exploring transcriptomic data
Omar Harb
New Feature Feedback

Exercise XV, Part 2: Exploring transcriptomic data with integrated searches Brian Brunk
Coffee Break

Group Exercise (includes presentations of shared strategies) All
Exit survey

EuPathDB Bioinformatics Resource Center — 2015 Workshop
For more information, email jckadmin@uga.edu.