To see details about the live ‘Methods for infectious disease modelling using genomics’ course and the original programme, you can refer to the course page and programme.

The contents table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainer
	Concepts in infectious disease modelling
	Introduction to infectious disease modelling	John Lees
	SIR models and surveillance	Yang Liu Leonie Lorenz
	When traditional epidemiological surveillance fails: Phylodynamics	Swapnil Mishra
	Interpreting scientific articles on modelling	John Lees Sonja Lehtinen Joel Hellewell Leonie Lorenz
	Pathogens and climate change – keynote presentation	Rachel Lowe
	Infectious disease modelling and tools and phylogenetic analysis
	Introduction to modelling in STAN	Timothy Russell, Víctor Rodríguez Bouza, Matt Russell
	Modelling pathogen evolution using odin.dust	Sonja Lehtinen Leonie Lorenz
	Nowcasting using EpiNow	Sam Abbott Joel Hellewell
	Modelling pangenome dynamics	John Lees Jacqueline Toussaint Leonie Lorenz Joel Hellewell
	Timed phylogenies and ancestral state reconstruction with BEAST2	Nicola De Maio Jacqueline Toussaint
	Data management and pathogen databases
	Responsible research data management	Ajay Mishra
	Biomodels database	Rahuman S. Malik Sheriff
	Pathogens portal	Nadim Rahman