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 |