Infectious Disease Genomic Epidemiology
Welcome
Welcome to Infectious Disease Genomic Epidemiology 2018.
The course schedule can be found here.
Pre-readings, pre-work, and laptop setup instructions can be found here.
We are using Google Classroom for discussion. Join the Class at https://classroom.google.com, select the “+” symbol in the upper right corner, click on “Join Class” and enter the class code provided to you.
The full course notes are available as a single PDF.
Class photo
Day 1
Welcome
Ann Meyer
Module 1: Introduction to Public Health Microbiology and Genomic Epidemiology
Will Hsiao
Lab Practical: Connecting to the Cloud
- We have set up 30 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows, please download this certificate.
Module 2: Pathogen Genomic Analysis I
Gary Van Domselaar
Module 3: Pathogen Genomic Analysis II
Dillon Baker
Keynote: Open Bioinformatics Takes a Centre Stage in Infectious Disease
Fiona Brinkman
Day 2
Module 4: Antimicrobial Resistance Genes
Andrew McArthur
Module 5: Phylogeographic Analysis
Anamaria Crisan
Bonus Bayesian Trees
Integrated Assignment
Day 3
Module 6: Emerging Pathogen Detection and Identification Using Metagenomics Samples
Gary Van Domselaar
Module 7: Data Visualization
Anamaria Crisan
Survey
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