EuPathDB Workshop

2016 Schedule

The course begins at 9:30 am on Monday, August 8th with a reception. The course will finish at 6:00 pm on Tuesday, August 9th.

Participants are expected to bring their own laptops to use in the workshop sessions.

Quick Links: EuPathDB | AmoebaDB | CryptoDB | FungiDB | GiardiaDB | HostDB | OrthoMCL DB | MicrosporidiaDB | PiroplasmaDB | PlasmoDB | ToxoDB | TrichDB | TriTrypDB

Instructors: Eve Basenko, Jessie Kissinger, Susanne Warrenfeltz

Time Event Instructor
Monday, August 8, 2016
9:30-9:45am General Workshop Introduction Eve Basenko, Jessie Kissinger, Susanne Warrenfeltz

Lecture: Omics Overview

Jessie Kissinger

Turbo Talks from Students

11:15-11:30am Morning Coffee Break
11:30-12:00am Introduction to EuPathDB sites and the search strategy system Susanne Warrenfeltz
12:00-1:00pm Lunch (provided)

Finding genes, examining gene pages and building search strategies

Eve Basenko, Susanne Warrenfeltz
3:00-3:15pm Afternoon Coffee Break

Browser I: The Genome Browser: alignments and comparative genomics

Jessie Kissinger
4:30-5:30pm Browser Exercise II: Interpreting RNAseq data

Advanced Browser II- on your own time

High resolution gbrowse image
Susanne Warrenfeltz
5:30-6:00pm Enrichments and Transformations: Tools for investigating your search results.
Eve Basenko
Tuesday, August 9, 2016
8:30-9:15am Isolates Jessica Kissinger
9:15-11:00am Functional Genomics 1: Transcriptomics and Proteomics Jessica Kissinger, Eve Basenko
10:15-10:30am coffee available
11:00am-12:00pm Functional Genomics 2: Host Response Susanne Warrenfeltz, Eve Basenko
12:00-1:00 Lunch (provided)
1:00-1:45pm Funcional Genomics 2: Host Response continued Susanne Warrenfeltz, Eve Basenko
1:45-3:00pm Sequence Exercises: Motifs, Domains and Colocation

Quick-Start: Regex Cheat Sheet
Links to Regular Expression Resources
Even more Regular Expression Help
Susanne Warrenfeltz, Eve Basenko
3:00-3:15pm Afternoon Coffee Break
3:15-4:30pm Population Genetics: SNPs

SNPs powerpoint
Susanne Warrenfeltz, Eve Basenko
4:30-5:15 Orthology and phylogenetic profiles
Susanne Warrenfeltz
5:15-5:30pm Workshop Survey
Susanne Warrenfeltz, Eve Basenko

EuPathDB Bioinformatics Resource Center -- 2016 Workshop
For more information, email