The course begins at 6:00 pm on Sunday, June 18th with a reception. The course will finish at 12:00 pm on Thursday, June 22nd.
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
| Time | Place | Event | Instructor |
|---|---|---|---|
| Sunday, June 18, 2017 | |||
| 6:00-9:00pm | University of Georgia Center for Continuing Education & Hotel Magnolia Ballroom, Salon 1 |
Registration and Welcome Dinner Workshop attendees and instructors introductions General introduction to EuPathDB and omics Transportation and Logistics Food and Activites in Athens #timetogoforvivax - Documentary about P vivax malaria from ICPVR 2017 in Manaus Brazil Photos taken during the workshop |
Brian Brunk, Alejandra Diaz, Diego Giraldo, Jessie Kissinger, Omar Harb, Susanne Warrenfeltz |
| Monday, June 19, 2017 | |||
| 7:00am onwards | Courtyard Cafe | Optional Breakfast - Use the coupons in your welcome packet | |
| 8:00am | Meet in the hotel lobby to leave for the workshop. | ||
| 8:20-9:00am | Life Sciences Room C128 |
General workshop introduction & introduction to EuPathDB functionality | Omar Harb |
| 9:00am-10:30am | Life Sciences Room C128 |
Finding genes, building search strategies and visiting gene pages |
Susanne Warrenfeltz |
| 10:30-10:45am | Life Sciences Room B116 |
Morning Coffee Break (provided) | |
| 10:45-11:45am | Life Sciences Room C128 |
Genome Browser I: Alignments and Comparative Genomics |
Susanne Warrenfeltz |
| 11:45am-12:00pm | Life Sciences Room C128 |
Glossary Survey Results |
Jessica Kissinger |
| 12:00-1:00pm | Life Sciences Room B116 |
Lunch | |
| 1:00-2:30pm | Life Sciences Room C128 |
Genome Browser II: Interpreting RNAseq data High resolution ToxoDB GBrowse | Brian Brunk Alejandra Diaz |
| 2:30-2:45pm | Life Sciences Room B116 |
Coffee/Tea Break (provided) | |
| 2:45-3:15pm | Life Sciences Room C128 |
Genome Browser II: Interpreting RNAseq data (Group Exercise) continued... | Brian Brunk Alejandra Diaz |
| 3:15-4:15pm | Life Sciences Room C128 |
Orthology and phylogenetic profiles |
Brian Brunk |
| 4:15-5:15pm | Life Sciences Room C128 |
RNA sequence data analysis via Galaxy, Part I Uploading data and starting the workflow (Group Exercise) TopHat Cufflinks Galaxy Project iPlant Collaborative |
Omar Harb |
5:15-5:45pm |
Life Sciences Room C128 |
Data retrieval and download | Susanne Warrenfeltz |
| 6:00-8:00pm | Coverdell Center Room 340 |
Reception and dinner | |
| Tuesday, June 20, 2017 | |||
| 7:00am onwards | Courtyard Cafe | Optional Breakfast - Use the coupons in your welcome packet | |
| 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 | Life Sciences Room C128 |
Genetics Exercises: Population genetics (SNPs) Brief Introduction: Population genetics (SNPs) |
Brian Brunk |
| As needed | Life Sciences Room B116 |
Coffee/Tea Available (provided) | |
| 11:30am-12:15pm | Life Sciences Room C128 |
Identifying SNPs using Galaxy, Part I (Group exercise) |
Omar Harb |
| 12:15-1:15pm | Life Sciences Room B116 |
Lunch (provided) | |
| 1:15-3:00pm | Life Sciences 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 | Life Sciences Room B116 |
Coffee/Tea Break (provided) | |
| 3:15-5:45pm | Life Sciences Room C128 |
Functional Genomics I: Transcriptomics, Proteomics, Go Enrichment, Metabolic Pathways Gene Ontology Enrichment Metabolic Pathways Use and misuse of the gene ontology annotations |
Brian Brunk |
| 5:45pm-6:30p | 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 21, 2017 | |||
| 7:00am onwards | Courtyard Cafe | Optional Breakfast - Use the coupons in your welcome packet | |
| 9:00-10:15am | Life Sciences Room C128 |
Annotation Exercise II: Viewing Companion results (Group Exercise) |
Susanne Warrenfeltz & Omar Harb |
| As needed | Life Sciences Room B116 |
Coffee/Tea Available (provided) | |
| 10:15-11:00am | Life Sciences Room C128 |
Isolates |
Jessica Kissinger |
| 11:00am-12:15pm | Life Sciences Room C128 |
Identifying SNPs using Galaxy, Part II: Viewing and analyzing your results (Group exercise) |
Omar Harb |
| 12:15-1:15pm | Life Sciences Room B116 |
Lunch (provided) | |
| 1:15-2:15pm | Life Sciences Room C128 |
Functional Genomics II: Host response data |
Susanne Warrenfeltz |
| 2:15-3:15 | Room C128 |
New Feature Feedback |
Susanne Warrenfeltz |
| 3:15-3:30pm | Life Sciences Room B116 |
Coffee/Tea Break | |
| 3:30-6:30pm | Life Sciences Room C128 |
Group Exercise I: Define your own questions and develop search strategies to answer them | Omar Harb Brian Brunk Ale Diaz Diego Giraldo Jessica Kissinger | Susanne Warrenfeltz
| 6:30 | Dinner on your own | ||
| Thursday, June 22, 2017 | |||
| 7:00am onwards | Courtyard Cafe | Optional Breakfast - Use the coupons in your welcome packet | |
| 9:00 - 10:00am | Life Sciences Room C128 |
Final Project, Part I, continued (Group exercise) | Omar Harb Brian Brunk Ale Diaz Diego Giraldo Jessica Kissinger Susanne Warrenfeltz |
| As needed | Life Sciences Room B116 |
Coffee/Tea Available (provided) | |
| 10:00-11:30am | Life Sciences Room C128 |
Final Project, Part II: Present shared strategies (Group exercise) | Students |
| 11:30-12:00pm | Life Sciences Room C128 |
Exit survey |
Omar Harb Brian Brunk Ale Diaz Diego Giraldo Jessica Kissinger Susanne Warrenfeltz |
| 12:00p | Life Sciences Room C128 |
Box lunches availalbe to go | |
