EuPathDB Workshop

2016 Schedule

The course begins at 4:00 pm on Monday, February 15th with a reception. The course will finish at 12:00 pm on Friday, February 19th.

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: Omar Harb, Stuart Ralph, David Roos and Chris Tonkin

Time Event
Monday, February 15, 2016
4:00-4:30pm Registration & Welcome
4:30-5:00pm General introduction to EuPathDB
5:00-6:00pm Student Turbo Presentations (2 min each)
6:00-8:00pm Dinner and Keynote Talk
Venue: WEHI, pizza dinner provided
Keynote speaker: Aaron Jex - Using next generation sequencing to investigate parasite genomes and transcriptomes
Tuesday, February 16, 2016

Gene Page Exercises: Finding genes, examining gene pages and building search strategies

10:30-10:45am Morning Coffee Break

Browser Exercise I: The Genome Browser: alignments and comparative genomics

12:00-1:00pm Lunch (provided)
1:00-3:30pm Browser Exercise II: Interpreting RNAseq data
High resolution gbrowse image
2:30-2:45pm Coffee Break
3:30-5:00pm Mapping Exercise I: RNA sequence data analysis (Part 1: Pathogen portal RNAseq pipeline) Group Exercise
5:00-6:00pm Keynote speaker: David S. Roos - Minning genomic databases
6:00-8:00pm Dinner
Venue: Naughtons Hotel, 43 Royal Parade, Parkville VIC 3052 (dinner at your own expense)
Wednesday, February 17, 2016
9:00-9:30am Introduction to SNPs in EuPathDB
9:30-11:00am Genetics Exercises: Population genetics (SNPs)
11:00-12:00pm Sequence Exercises: Motifs and domains
Quick-Start: Regex Cheat Sheet
Links to Regular Expression Resources
Even more Regular Expression Help
12:00-1:00pm Lunch (provided)

Annotation Exercise I: Using Companion to annotate an assembled genome (Group Exercise)

2:00-3:00pm Orthology Exercises: Orthology and phylogenetic profiles
3:00-3:15pm Coffee Break
3:15-5:00pm Mapping Exercise II: RNA sequence data analysis (Part 2 (Group Exercise): viewing and analyzing your results)

Galaxy Project
iPlant Collaborative
5:00-6:00pm Genome Ontology Enrichment
Metabolic Pathways
6:00-8:00pm Dinner and Keynote Talk
Venue: Tsubu, Gate 6, Building 1888 ,Swanston St, University of Melbourne (dinner at your own expense)
Keynote Speaker: Kaylene Simpson - Functional Genomics to study host-pathogen interactions
Thursday, February 18, 2016
9:00-10:00am Annotation Exercise II: Viewing Companion results (Group Exercise)
10:00-12:15am Functional Genomics I:

12:15-1:15pm Lunch
1:15-2:15pm Functional Genomics II: Host response data
2:15-2:30pm Coffee Break
2:30-4:45pm Group Exercise I: Define your own questions and develop search strategies to answer them
4:45-5:45pm Keynote Talk
Venue: WEHI
Keynote speaker: Alicia Oshlack - Designing and Analysing RNASeq experiments
6:00-8:00pm Dinner (provided)
Princes Hill Bowls Club 109 Bowen Crescent, Carlton North VIC 3054 (Tram 19)
Friday, February 19, 2016
9:00-10:30am Group Exercise II: Continue developing your questions and prepare to present results
10:30-11:45am Group Presentations
11:45-12:00pm Exit survey
12:00pm Lunch

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