2019 Schedule


The course begins at 6:00 pm on Sunday, June 2nd with a reception. The course will finish at 12:00 pm on Thursday, June 6th.

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 2, 2019
6:00-9:00pm Holiday Inn Athens-University Area - across the street from SpringHill Suites Registration and Welcome Dinner
Omics talk and attendees introductions
General introduction to omics
Transportation and Logistics
Brian Brunk,
Jessie Kissinger,
Omar Harb,
Susanne Warrenfeltz
Monday, June 3, 2019
6:30am onwards SpringHill Suites by Marriott Athens Downtown/University Area Optional Breakfast Provided
8:00am Meet in the hotel lobby to leave for the workshop. There are options for walking or taking the bus which will be explained during the Sunday night reception and lecture.
8:30am 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
12:30pm Life Sciences
Room B116
Lunch (provided)
1:30pm Life Sciences
Room C128
RNA sequence data analysis via Galaxy, Part I Uploading data (Group Exercise)

TopHat
Cufflinks
Galaxy Project
Omar Harb
2:15pm Life Sciences
Room C128
Genome Browser II: Interpreting RNAseq data
High resolution ToxoDB GBrowse
Brian Brunk
3:30pm Life Sciences
Room B116
Coffee/Tea Break (provided)
4:00pm Life Sciences
Room C128
Orthology and Phylogenetic Profile

Jessica Kissinger
5:15pm Life Sciences
Room C128
RNA sequence data analysis via Galaxy, Part I starting the workflow (Group Exercise)

TopHat
Cufflinks
Galaxy Project
Omar Harb
6:00-8:00pm Coverdell Center
Room 340
Informal reception and dinner
Coverdell Center, a short walk from the workshop location

Tuesday, June 4, 2019
6:30am onwards SpringHill Suites by Marriott Athens Downtown/University Area Optional Breakfast Provided
8:00am Meet in the hotel lobby to leave for the workshop.
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

Reg Ex Links
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
12:00pm Life Sciences
Room B116A
Lunch (provided) and Special Seminar, Patricia Johnson
"Host-pathogen interactions between the sexually-transmitted parasite Trichomona vaginalis and its human host," Patricia Johnson, UCLA.

1:15pm Life Sciences
Room C128
RNA sequence data analysis Part 1a: Cufflinks and Exporting your data to EuPathDB

RNA sequence data analysis Part 2: viewing and analyzing your results (Group Exercise)

FastQC Result Interpretation
Beginner DESeq2 guide
FastQC output
SNP Eff manual
Trimmomatic Manual
Omar Harb
3:00pm Life Sciences
Room B116
Coffee/Tea Break (provided)
3:15pm Life Sciences
Room C128
Functional Genomics 1: Transcriptomics, Proteomics, GO Enrichment, Metabolic Pathways

Brian Brunk
5:45pm Life Sciences
Room C128
Annotation Exercise 1: Using Companion to annotate an assembled genome (Group Exercise)

Companion info
Susanne Warrenfeltz
6:30pm Dinner on your own
Wednesday, June 5, 2019
6:30am onwards SpringHill Suites by Marriott Athens Downtown/University Area Optional Breakfast Provided
8:30am Meet in the hotel lobby to leave for the workshop.
9:00am Life Sciences
Room C128
Annotation Exercise 2: Viewing Companion results (Group Exercise)

Companion results
Susanne Warrenfeltz
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
Identifying SNPs using Galaxy, Part 2: Viewing and analyzing your results (Group exercise)

SNPEff manual

Trimmomatic Manual
Omar Harb
12:15pm Life Sciences
Room B116
Lunch (provided)
1:15pm Life Sciences
Room C128
Identifying SNPs using Galaxy, Part 2: Viewing and analyzing your results (Group exercise) Omar Harb
1:45pm Life Sciences
Room C128
Functional Genomics 2: Host response data
Susanne Warrenfeltz
2:45pm Life Sciences
Room B116
Data retrieval and download Susanne
3:15pm Life Sciences
Room B116
Coffee/Tea Available (provided)
3:30pm Life Sciences
Room C128
Final Project, Part 1: Define your own questions and develop search strategies to answer them (Group exercise) Omar Harb
Brian Brunk
Jessica Kissinger
Susanne Warrenfeltz
6:30pm Dinner on your own
Thursday, June 6, 2019
6:30am onwards SpringHill Suites by Marriott Athens Downtown/University Area Optional Breakfast Provided
8:30am Meet in the hotel lobby to leave for the workshop.
9:00am Life Sciences
Room C128
Final Project, Part 1, continued... Omar Harb
Brian Brunk
Jessica Kissinger
Susanne Warrenfeltz
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
12:00pm Life Sciences
Room C128
Box lunches availalbe to go

EuPathDB Bioinformatics Resource Center — 2019 Workshop
For more information, email jckadmin@uga.edu.