2018 Schedule


The course begins at 6:00 pm on Sunday, June 17th with a reception. The course will finish at 12:00 pm on Thursday, June 21st.

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 UGA Center for Continuing Education and 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: Brian Brunk, Omar Harb, Jessica Kissinger, Susanne Warrenfeltz, Sheena Shah-Simpson

Time Place Event Instructor
Sunday, June 17, 2018
6:00-9:00pm University of Georgia Center for Continuing Education & Hotel
Registration and Welcome Dinner
Omics talk and attendees introductions
General introduction to omics
Transportation and Logistics
Brian Brunk,
Jessie Kissinger,
Omar Harb,
Susanne Warrenfeltz
Sheena Shah-Simpson
Monday, June 18, 2018
7:00am onwards Georgia Center Hotel's Courtyard Cafe
first floor of hotel
Optional Breakfast - Use the coupons in your welcome packet
8:00am Meet in the hotel lobby to leave for the workshop.
8:20am Life Sciences
Room C128
Workshop set up & EuPathDB general introduction Omar Harb
9:00am Life Sciences
Room C128
Vocabulary Survey Results Jessica Kissinger
9:15am Life Sciences
Room B116
Finding genes, building search strategies and visiting gene pages Susanne Warrenfeltz
10:30am Life Sciences
Room C128
Morning Coffee Break (provided)
10:45am Life Sciences
Room B116
Finding genes, building strategies and visiting gene pages -- Continued Susanne Warrenfeltz
11:00am Life Sciences
Room C128
Genome Browser I: Alignments and Comparative Genomics Susanne Warrenfeltz
12:00pm Life Sciences
Room B116
Lunch (provided)
1:00pm Life Sciences
Room C128
Genome Browser II: Interpreting RNAseq data
High resolution ToxoDB GBrowse
Brian Brunk
2:30pm Life Sciences
Room B116
Coffee/Tea Break (provided)
2:45 Life Sciences
Room C128
Genome Browser 2: Interpreting RNAseq data (Group Exercise) continued... Brian Brunk
4:15pm Life Sciences
Room C128
RNA sequence data analysis via Galaxy, Part I Uploading data and starting the workflow (Group Exercise)

TopHat
Cufflinks
Galaxy Project
Omar Harb
5:15pm Life Sciences
Room C128
Data retrieval and download Susanne Warrenfeltz
6:00-8:00pm Coverdell Center
Room 340
Informal reception and dinner
Coverdell Center, a short walk, between hotel and workshop

Tuesday, June 19, 2018
7:00am onwards Georgia Center Hotel's Courtyard Cafe
first floor of hotel
Optional Breakfast - Use the coupons in your welcome packet
8:20am Meet in the hotel lobby to leave for the workshop. Or walk on your own
8:30am 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
9:45am Life Sciences
Room C128
Genetics Exercises: Population genetics (SNPs)
Brief Introduction: Population genetics (SNPs)
Brian Brunk
As needed
starting at 10am
Life Sciences
Room B116
Coffee/Tea Available (provided)
11:30am Life Sciences
Room C128
Identifying SNPs using Galaxy, Part I (Group exercise)
Omar Harb
12:15pm Life Sciences
Room B116
Lunch (provided)
1:15pm Life Sciences
Room C128
RNA sequence data analysis Part II: viewing and analyzing your results (Group Exercise)

FastQC Result Interpretation
Omar Harb
3:00pm Life Sciences
Room B116
Coffee/Tea Break (provided)
3:15pm Life Sciences
Room C128
Functional Genomics I: Transcriptomics, Proteomics, Go Enrichment, Metabolic Pathways

Brian Brunk
as you like Life Sciences
Room C128
Orthology and Phylogenetic Profile

5:45pm Life Sciences
Room C128
Annotation Exercise I: Using Companion to annotate an assembled genome (Group Exercise)

Companion info
Susanne Warrenfeltz & Omar Harb
6:30pm Dinner on your own
Wednesday, June 20, 2018
7:00am onwards Georgia Center Hotel's Courtyard Cafe
first floor of hotel
Optional Breakfast - Use the coupons in your welcome packet
8:50am Meet in the hotel lobby to leave for the workshop. Or walk on your own
9:00am Life Sciences
Room C128
Annotation Exercise II: Viewing Companion results (Group Exercise)
Susanne Warrenfeltz & Omar Harb
As needed
starting at 10am
Life Sciences
Room B116
Coffee/Tea Available (provided)
10:15am Life Sciences
Room C128
Isolates
Jessica Kissinger
11:00am Life Sciences
Room C128
Discuss the Orthology Profile search and Companion results Omar Harb
12:15pm Life Sciences
Room B116
Lunch (provided)
1:15pm Life Sciences
Room C128
Identifying SNPs using Galaxy, Part II: Viewing and analyzing your results (Group exercise)

SNPEff manual

Trimmomatic Manual
Omar Harb
3:00pm Life Sciences
Room C128
Functional Genomics II: Host response data
Susanne Warrenfeltz
3:15pm Life Sciences
Room B116
Coffee/Tea Break
3:30pm Life Sciences
Room C128
Final Project, Part I: Define your own questions and develop search strategies to answer them (Group exercise) Omar Harb
Brian Brunk
Jessica Kissinger
Susanne Warrenfeltz
Sheena Shah-Simpson
6:30pm Dinner on your own
Thursday, June 21, 2018
7:00am onwards Courtyard Cafe Optional Breakfast - Use the coupons in your welcome packet
8:50am Meet in the hotel lobby to leave for the workshop. Or walk on your own
9:00am Life Sciences
Room C128
Final Project, Part 1, continued... Omar Harb
Brian Brunk
Jessica Kissinger
Susanne Warrenfeltz
Sheena Shah-Simpson
10:00am Life Sciences
Room C128
Final Project, Part 2, Present shared strategies...
As needed
starting at 10am
Life Sciences
Room B116
Coffee/Tea Available (provided)
11:30pm Life Sciences
Room C128
Workshop Feedback
Omar Harb
Brian Brunk
Jessica Kissinger
Susanne Warrenfeltz
Sheena Shah-Simpson
12:00pm Life Sciences
Room C128
Box lunches availalbe to go

EuPathDB Bioinformatics Resource Center — 2018 Workshop
For more information, email jckadmin@uga.edu.