2016 Schedule

The course begins at 6:30 pm on Sunday, June 12th with a reception. The course will finish at 12:00 pm on Thursday, June 16th.

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 the lobby.

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

Instructors: Eve Basenko, Brian Brunk, Omar Harb, Jessica Kissinger, Susanne Warrenfeltz

Time Place Event Instructor
Sunday, June 12, 2016
6:30-9:00pm Holiday Inn
Georgian Ballroom
Registration & Welcome Reception
General introduction to EuPathDB and omics
Workshop attendees and instructors introductions
Transportation and Logistics
Jessie Kissinger,
Omar Harb,
Susanne Warrenfeltz
Monday, June 13, 2016
available starting 6:30am Holiday Inn Redfearn Grille Optional Breakfast (breakfast coupons provided in welcome packet)
8:30-8:45am Life Sciences Room C128 General Workshop Introduction Omar Harb, Susanne Warrenfeltz
8:45-9:15am Room C128 Site Usability Exercise Susanne Warrenfeltz
9:15-10:00am Room C128 Introduction to EuPathDB sites and the search strategy system Omar Harb
10:00-10:15am Room B116 Morning Coffee Break (provided)
10:15-11:45pm Room C128

Finding genes, building search strategies and visiting gene pages

Susanne Warrenfeltz
11:45-12:00pm Room C128

Glossary Survey Results

Jessica Kissinger
12:00-1:00pm Room B116 Lunch (provided)
1:00-2:15pm Room C128

Genome Browser I: Alignments and Comparative Genomics

Susanne Warrenfeltz
2:15-2:30pm Room B116 Coffee Break (provided)
2:30-4:15pm Room C128 Genome Browser II: Interpreting RNAseq data

High resolution ToxoDB GBrowse

Brian Brunk
4:15-5:15pm Room C128 RNA sequence data analysis via Galaxy, Part I Uploading data and starting the workflow (Group Exercise)

Galaxy Project
iPlant Collaborative
Omar Harb

Room C128 Data retrieval and download Eve Basenko
6:00-8:00pm Coverdell Center
Room 340
Dinner (provided)
Tuesday, June 14, 2016
available starting 6:30am Holiday Inn Redfearn Grille Optional Breakfast
8:30-9:45am Life Sciences Room C128 Sequence Exercises: Motifs, domains and colocation
Introduction: Regular Expressions
Quick-Start: Regex Cheat Sheet
Links to Regular Expression Resources
Even more Regular Expression Help
Omar Harb
9:45-11:30am Room C128 Genetics Exercises: Population genetics (SNPs)
Brief Introduction: Population genetics (SNPs)
Brian Brunk
10:30-10:45 Room B116 Coffee Available (provided)
11:30-12:15pm Room C128 Orthology and phylogenetic profiles
Susanne Warrenfeltz
12:15-1:15pm Room B116 Lunch (provided)
1:15-3:00pm Room C128 RNA sequence data analysis Part II: viewing and analyzing your results (Group Exercise)
FastQC Result Interpretation
CuffDiff Paper
Omar Harb
3:00-3:15pm Room B116 Coffee Break (provided)
3:15-4:15pm Room C128 Gene Ontology Enrichment

Metabolic Pathways

Use and misuse of the gene ontology annotations
Eve Basenko
4:15pm-5:15 Room C128 Annotation Exercise I: Using Companion to annotate an assembled genome (Group Exercise)

Omar Harb
5:15-6:00pm Room C128 Isolates Jessica Kissinger
Wednesday, June 15, 2016
available starting 6:30am Holiday Inn Redfearn Grille Optional Breakfast
9:00-10:00am Life Sciences Room C128 Annotation Exercise II: Viewing Companion results (Group Exercise)
Omar Harb
10:00-12:15am Room C128 Functional Genomics I: Transcriptomics and Proteomics
Brian Brunk
starting at 10:30am Room B116 Coffee Available
12:15-1:15 Room B116 Lunch (provided)
1:15-2:15pm Room C128 Functional Genomics II: Host response data
Brian Brunk
Susanne Warrenfeltz
2:15-3:15 Room C128 New Feature Feedback
Susanne Warrenfeltz
3:15-3:30pm Room B116 Coffee Break
3:30-5:30pm Room C128 Group Exercise I: Define your own questions and develop search strategies to answer them Omar Harb
Eve Basenko
Brian Brunk
Susanne Warrenfeltz
Dinner on your own

Thursday, June 16, 2016
available starting 6:30am Holiday Inn Redfearn Grille Optional Breakfast
9:00-11:30am Life Sciences Room C128 Group Exercise II - present shared strategies
Omar Harb
Eve Basenko
Brian Brunk
Susanne Warrenfeltz
11:30-12:00pm Room C128 Exit survey
Omar Harb
Jessica Kissinger
Eve Basenko
Brian Brunk
Susanne Warrenfeltz

EuPathDB Bioinformatics Resource Center — 2016 Workshop
For more information, email jckadmin@uga.edu.