Armidale Animal Breeding Summer Course 2018
Venue: University
of New England, Armidale, NSW Australia
Course Audience: Postgraduate
students and other professionals
Mathematical modeling of infection dynamics
in genetically diverse livestock populations
Teachers: Andrea
Doeschl-Wilson and Osvaldo Anacleto
The Roslin Institute
Edinburgh, Scotland
Dates: Monday 5 February 2018 (9am) – Thursday 8 February 2018 (4pm)
Course Materials 2018
Day 1 (Monday): General introduction to mathematical
modelling & to key concepts for infectious diseases in livestock
Lecture 1: Introduction
to mathematical modelling (A. Wilson)
Lecture 2: Infectious disease
fundamentals (A. Wilson)
Lecture 3: Examples of
infectious disease models for livestock (A. Wilson)
Tutorial 1: Designing a mathematical model
for bovine Tuberculosis
Tutorial 2: Introduction to probability
distributions & R
Intro to R Intro to R
Day 2 (Tuesday):
Modelling epidemics (A. Wilson)
Lecture 4: Mathematical essentials
Lecture 5: Deterministic models for
homogeneous populations
Tutorial L5: Deterministic models for homogeneous
populations
Lecture 6: Deterministic models in
heterogeneous populations
Tutorial L6: Deterministic models for heterogeneous
populations
Lecture 7: Stochastic & individual based
epidemiological models
Tutorial L7: Stochastic models
Day 3
(Wednesday): Mathematical models of within host infection dynamics (AW)
Lecture 8: Empirical vs mechanistic
models of within-host infection dynamics
Tutorial L8: Exploring empirical & mechanistic
models of within-host infection dynamics
R-Code Tutorial Within Host Models
Statistical
interference: estimating model parameters (O. Anacleto)
Tutorial L9: Frequentist inference for
proportions & stochastic epidemic models
Day 4
(Thursday): Bayesian interference (O. Anacleto)
Lecture 10: Introduction to Bayesian inference &
conjugate models
Tutorial L10: Bayesian inference for
the beta-binomial model
Tutorial
L11: Markov chains
Lecture 12: Applications of Bayesian inference using
MCMC
Tutorial L12: Analysis of a
hierarchical non-linear model for PRRS data
2018 Course
Material of previous years:
Armidale Genetics Summer Course 2017 Materials
·
Genotype by environment interaction in breeding
programs: Piter Bijma and Han Mulder
Armidale Genetics Summer Course 2016 Materials
Investigating
the Genetic Architecture of Complex Traits
& Prediction of Phenotype
from
Genome-wide SNPs - Doug
Speed and David Balding
Armidale Animal Breeding Summer Course 2015 Materials
•
Primer to genomic
analysis using R:
Cedric Gondro
•
From Sequence Data to
Genomic Prediction: Ben Hayes
and Hans Daetwyler
Armidale Animal Breeding Summer Course 2014 Materials
Breeding Program Design with Genomic Selection: Jack Dekkers,
Julius van der Werf
Armidale Animal Breeding Summer Course 2012 Materials
Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de
los Campos
Armidale Animal Breeding Summer Course 2011 Materials
·
Statistical methods and design in
plant breeding and genomics: Ian Mackay
·
IBD inference in genome association
studies: Elizabeth Thompson
Armidale Animal Breeding Summer Course 2010 Materials
·
Application of
evolutionary algorithms to solve complex problems in quantitative genetics
and
bioinformatics: Brian Kinghorn, Cedric Gondro
·
Bayesian methods in genome association studies: Dorian Garrick, Rohan
Fernando
Armidale Animal Breeding Summer Course 2009 Materials
·
Quantitative
Genetic Theory and Analysis- Selection
Theory: Bruce
Walsh
·
Quantitative
Genetic Models for social interaction and inherited variability: Piter
Bijma
Armidale Animal Breeding Summer Course 2008 Materials
·
Genomic
Selection: Ben Hayes
Armidale Animal Breeding Summer Course 2007 Materials
·
Generalized Linear Mixed Models:
Steve Kachman
Armidale Animal Breeding Summer Course 2006 Materials
·
Gene Expression:
Toni Reverter
·
Breeding Program Design:
Graser,
James, Van der Werf
Armidale Animal Breeding Summer Course 2003 Materials