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 | |
