Pre-Workshop Module

These pre-workshop exercises cover some of the basic functionality in VEuPathDB. Please complete the exercises included in the module prior to the start of the workshop on June 7th. We expect that this module will take 2 - 2.5 hours to complete. The instructors will assume that all attendees have completed these exercises prior to the start of the workshop.

Pre-workshop-module.pdf

Schedule

Module pdf files will be linked to the schedule just before the session begins

Instructors: Omar Harb, Jessica Kissinger, Susanne Warrenfeltz, Kathryn Crouch, Mark Hickman, Sam Rund, Gloria I. Giraldo-Calderón, Evelina Basenko, Uli Boehme, David Starns, Sarah Kelly, Beatrice Amos, Mary Ann McDowell, David Roos

Time Event Instructor
Monday, June 7th
All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/.
8:30am Zoom session opens for discussion
9 - 9:10am Workshop Introduction Jessie Kissinger
9:10 - 9:15am Welcome and introductions Mary Ann McDowell and David Roos
9:15 - 9:55am Introductions Everyone - Name, organisms of research, geographic location
10 - 10:05am short break
10 - 10:10am Transcriptomics and Proteomics lecture
Trans-and-Prot-lecture-slides.pdf
Susanne Warrenfeltz
10:10am - 12:00pm Break out rooms for hands on work - transcriptomics and proteomics
Transcriptomics.pdf
Proteomics.pdf
12:00 - 12:45pm Lunch Break
12:45 - 1:00pm Gene ontology and enrichment lecture
GO-Term-presentation.pdf
Omar Harb
1:00 - 1:30pm Break out rooms for hands on work - GO enrichment
GO-Enrichment.pdf
1:30 - 1:50pm Galaxy/RNAseq lecture
RNAseq_lecture.pdf
Kathryn Crouch
1:50 - 3:00pm Break out rooms for hands on work - RNAseq Galaxy part 1
Galaxy-RNAseq-datasets.pdf
Galaxy-RNAseq-instructions.pdf
3 - 3:30pm Optional discussion and question time
Tuesday, June 8th
All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/.
8:30am Zoom session opens for discussion
9:00 - 9:10am Phenotype exercise lecture Evelina Basenko
9:10 - 10:00am Break out rooms for hands on work - Phenotype
Phenotype-Exercise.pdf
10:00 - 10:20am Gene models lecture David Roos
10:20 - 11:30am Break out rooms for hands on work - Adv. JBrowse gene models
Adv-JBrowse-gene-models.pdf
11:30am - 12:00pm Group discussion with some students highlighting what they found
12:00pm Lunch Break
1:00 - 1:20pm Lecture RNAseq pipeline output, Fastq and DESeq2 Mark Hickman
1:20 - 3:00pm Break out rooms for hands on work - RNAseq Galaxy part 2
Galaxy-RNAseq-Part2.pdf
3 - 3:30pm Optional discussion and question time
Wednesday, June 9th
All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/.
8:30am Zoom session opens for discussion
9:00 - 9:20am Orthology lecture David Roos
9:20 - 10:15am Break out rooms for hands on work - orthology
Orthology-module.pdf
10:15 - 10:30am Lecture on variation - SNPs and CNVs
Variation-Lecture.pdf
Kathryn Crouch
10:30am - 12:00pm Break out rooms for hands on work - SNPs and CNVs
SNP-and-CNV-module.pdf
12:00pm Lunch Break
1:00pm Colocation and Introduction to group projects Omar Harb
1:30 - 3:00pm Break out rooms for hands on work - Group project
3 - 3:30pm Optional discussion and question time
Thursday, June 10th
All times in this schedule are given as Eastern Daylight time. Please convert to your location https://www.thetimezoneconverter.com/.
8:30am Zoom session opens for discussion
9:00 - 9:10am Metabolic pathways lecture
Metabolic-pathways-lecture.pdf
Jessie Kissinger
9:10 - 10:00am Break out rooms for hands on work - Metabolic pathways
Metabolic-pathways-module.pdf
10:00 - 10:05am Short break
10:05 - 12pm Break out rooms for hands on work - Group project
12:00pm Lunch Break
Breakout rooms can stay open for continued group project work
1:00 - 2:30pm Final Project presentations
2:30 - 3:00pm Workshop wrapup and final thoughts
3 - 3:30pm Optional discussion and question time

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


VEuPathDB Bioinformatics Resource Center — 2021 Workshop
For more information, email jckadmin@uga.edu.