Skip to content

Latest commit

 

History

History
196 lines (123 loc) · 7.33 KB

IDE_2024.md

File metadata and controls

196 lines (123 loc) · 7.33 KB
Raw
layout permalink title header1 header2 image keywords description instructors length
workshop_main_4day
/IDE_2024
Infectious Disease Genomic Epidemiology 2024
Workshop Pages for Students
Infectious Disease Genomic Epidemiology 2024
/site_images/CBW_epidemiology_icon.png
Infectious Disease Genomic Epidemiology
Infectious Disease Genomic Epidemiology
5 days

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 May 10th can be found here.
The schedule for this session can be found here.

Class Photo

Infectious Disease Genomic Epidemiology Class of 2024

Day 1

Virtual Welcome

Nia Hughes

AWS Setup

Zhibin Lu

You can find the instructions here.

Module 1: Introduction to Genomic Epidemiology

William Hsiao

Module 1 Lecture Recording
Module 1 Lecture Slides

Module 2: De Novo Genome Assembly and Annotation

Gary Van Domselaar

Module 2 Lecture Recording
Module 2 Lecture Slides

Lab

Module 2 Lab

Integrative Assignment

Integrative Assignment 1 | Answer Key
Integrative Assignment 2 | Answer Key

Day 2

Module 3: Data Curation and Data Sharing

Emma Griffiths

Module 3 Lecture Recording
Module 3 Lecture Slides

Lab

Module 3 Lab
Module 3 Lab Instructions

Module 4: Phylogenetic Analysis

Fiona Brinkman

Module 4 Lecture Recording
Module 4 Lecture Slides

Day 3

Module 5: Viral Pathogen Genomic Analysis - Single Nucleotide Variants

Jared Simpson

Module 5 Lecture Recording
Module 5 Lecture Slides

Lab

Module 5 Lab

Module 6: Bacterial Pathogen Genomic Analysis - Genome-based Subtyping

Ed Taboada

Module 6 Lecture Recording
Module 6 Lecture Slides

Lab

Module 6 Lab

Day 4

Module 7: Antimicrobial Resistant Gene (AMR) Analysis

Andrew McArthur

Module 7 Lecture Recording
Module 7 Lecture Slides

Lab

Module 7 Lab

Module 8: Phylodynamics

Finlay Maguire

Module 8 Lecture Recording
Module 8 Lecture Slides

Lab

Module 8 Lab

Day 5

Module 9: Mobile Genetic Elements

Rob Beiko

Module 9 Lecture Recording
Module 9 Lecture Slides

Lab

Module 9 Lab Instructions
Module 9 Lab Slides
Data file: MicroReactMatrix.tsv
Data file: Module9-core_gene_alignment.tre

Module 10: Emerging Pathogen Detection and Identification

Darian Hole

Module 10 Lecture Recording
Module 10 Lecture Slides

Lab

Module 10 Lab
Module 10 Lab Slides

Post-Workshop Materials

CourseData

Note that some of these files are quite large. If you have issues downloading them, try copying the link address, opening a new blank tab, and entering the URL into the new tab's address bar. If that fails, 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_IDE_240509
  • AMI ID: ami-09493b543784a1309

If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.