The course begins at 6:30 pm on Sunday, June 12th with a reception. The course will finish at 12:00 pm on Thursday, June 16th.
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 Holiday Inn
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: Eve Basenko, Brian Brunk, Omar Harb, Jessica
Kissinger, Susanne Warrenfeltz
| Time | Place | Event | Instructor |
|---|---|---|---|
| Sunday, June 12, 2016 | |||
| 6:30-9:00pm | Holiday Inn Georgian Ballroom |
Registration & Welcome Reception General introduction to EuPathDB and omics Workshop attendees and instructors introductions Transportation and Logistics |
Jessie Kissinger, Omar Harb, Susanne Warrenfeltz |
| Monday, June 13, 2016 | |||
| available starting 6:30am | Holiday Inn Redfearn Grille | Optional Breakfast (breakfast coupons provided in welcome packet) | |
| 8:30-8:45am | Life Sciences Room C128 | General Workshop Introduction | Omar Harb, Susanne Warrenfeltz |
| 8:45-9:15am | Room C128 | Site Usability Exercise | Susanne Warrenfeltz |
| 9:15-10:00am | Room C128 | Introduction to EuPathDB sites and the search strategy system | Omar Harb |
| 10:00-10:15am | Room B116 | Morning Coffee Break (provided) | |
| 10:15-11:45pm | Room C128 |
Finding genes, building search strategies and visiting gene pages |
Susanne Warrenfeltz |
| 11:45-12:00pm | Room C128 |
Glossary Survey Results |
Jessica Kissinger |
| 12:00-1:00pm | Room B116 | Lunch (provided) | |
| 1:00-2:15pm | Room C128 |
Genome Browser I: Alignments and Comparative Genomics |
Susanne Warrenfeltz |
| 2:15-2:30pm | Room B116 | Coffee Break (provided) | |
| 2:30-4:15pm | Room C128 | Genome Browser II: Interpreting RNAseq data High resolution ToxoDB GBrowse | Brian Brunk |
| 4:15-5:15pm | 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 |
Room C128 | Data retrieval and download | Eve Basenko |
| 6:00-8:00pm | Coverdell Center Room 340 |
Dinner (provided) | |
| Tuesday, June 14, 2016 | |||
| available starting 6:30am | Holiday Inn Redfearn Grille | Optional Breakfast | |
| 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 | Room C128 |
Genetics Exercises: Population genetics (SNPs) Brief Introduction: Population genetics (SNPs) |
Brian Brunk |
| 10:30-10:45 | Room B116 | Coffee Available (provided) | |
| 11:30-12:15pm | Room C128 | Orthology and phylogenetic profiles |
Susanne Warrenfeltz |
| 12:15-1:15pm | Room B116 | Lunch (provided) | |
| 1:15-3:00pm | 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 | Room B116 | Coffee Break (provided) | |
| 3:15-4:15pm | Room C128 |
Gene Ontology Enrichment Metabolic Pathways Use and misuse of the gene ontology annotations |
Eve Basenko |
| 4:15pm-5:15 | Room C128 | Annotation Exercise I: Using Companion to annotate an assembled genome (Group Exercise) |
Omar Harb |
| 5:15-6:00pm | Room C128 | Isolates | Jessica Kissinger |
| Wednesday, June 15, 2016 | |||
| available starting 6:30am | Holiday Inn Redfearn Grille | Optional Breakfast | |
| 9:00-10:00am | Life Sciences Room C128 | Annotation Exercise II: Viewing Companion results (Group Exercise) |
Omar Harb |
| 10:00-12:15am | Room C128 |
Functional Genomics I: Transcriptomics and Proteomics |
Brian Brunk |
| starting at 10:30am | Room B116 | Coffee Available | |
| 12:15-1:15 | Room B116 | Lunch (provided) | |
| 1:15-2:15pm | Room C128 | Functional Genomics II: Host response data |
Brian Brunk Susanne Warrenfeltz |
| 2:15-3:15 | Room C128 | New Feature Feedback |
Susanne Warrenfeltz |
| 3:15-3:30pm | Room B116 | Coffee Break | |
| 3:30-5:30pm | Room C128 | Group Exercise I: Define your own questions and develop search strategies to answer them | Omar Harb Eve Basenko Brian Brunk Susanne Warrenfeltz |
| 5:30 | Dinner on your own |
||
| Thursday, June 16, 2016 | |||
| available starting 6:30am | Holiday Inn Redfearn Grille | Optional Breakfast | |
| 9:00-11:30am | Life Sciences Room C128 | Group Exercise II - present shared strategies |
Omar Harb Eve Basenko Brian Brunk Susanne Warrenfeltz |
| 11:30-12:00pm | Room C128 | Exit survey |
Omar Harb Jessica Kissinger Eve Basenko Brian Brunk Susanne Warrenfeltz |
