Infectious Disease Genomic Epidemiology 2023
Welcome
The course schedule can be found here
Meet your faculty here
Pre-Workshop Materials
Pre-work including programs to install can be found here
AWS Module
Please follow the instructions to log into your AWS instance.
The content for our AWS/Unix review session on April 17th can be found here.
The schedule for this session can be found here.
Class Photo
Infectious Disease Genomic Epidemiology Class of 2023
Day 1
Virtual Welcome
Nia Hughes
Module 1: Introduction to Genomic Epidemiology
William Hsiao
Module 1 Lecture Recording
Module 1 Lecture Slides
Module 2: Phylogenetic Analysis
Fiona Brinkman
Module 2 Lecture Recording
Module 2 Lecture Slides
AWS Setup
Zhibin Lu
You can find the instructions here.
Module 3: Data Curation and Data Sharing
Emma Griffiths
Module 3 Lecture Recording
Module 3 Lecture Slides
Lab
Day 2
Module 4: Viral Pathogen Genomic Analysis - Single Nucleotide Variants
Jared Simpson
Module 4 Lecture Recording
Module 4 Lecture Slides
Lab
Module 5: Bacterial Pathogen Genomic Analysis
Ed Taboada
Module 5 Lecture Recording
Module 5 Lecture Slides
Lab
Module 5 Lab Setup
Module 5 Lab
Day 3
Module 6: Antimicrobial Resistant Gene (AMR) Analysis
Andrew McArthur
Module 6 Lecture Recording
Module 6 Lecture Slides
Lab
Module 7: Phylodynamics and Transmission Dynamics
Finlay Maguire
Module 7 Lecture Recording
Module 7 Lecture Slides
Lab
Day 4
Module 8: Emerging Pathogen Detection and Identification
Aaron Petkau
Module 8 Lecture Recording
Module 8 Lecture Slides
Lab
Module 8 Lab Module 8 Lab Slides
Keynote Lecture | Follow That Virus!: Genomics Leading the Way
Dr. Samira Mubareka
Keynote Lecture Recording
Keynote Lecture Slides
Module 9: Mobile Genetic Elements and Environmental Microbiome
Gary Van Domselaar
Module 9 Lecture Recording
Module 9 Lecture Slides
Lab
Post-Workshop Materials
CourseData
Note that some of these files are quite large. If you have issues downloading them, contact us at support@bioinformatics.ca.
AMI
We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on how to launch an EC2 instance from a custom Amazon Machine Image. Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.
Here are the details of the AMI:
- AWS Region: us-east-1 (N. Virgina)
- AMI type: public image
- AMI name: CBW_230416
- AMI ID: ami-0b905fa1d1d233a17
If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.
Software
For information on installing the necessary tools, please visit