Armidale Animal Breeding Summer Course 2004

Venue:    University of New England, Armidale, NSW Australia
Dates:     Date: 10-19 February 2004
 

                                               click on topic for more detail, materials and slides

    Photos:  Course participants (Modules B)              Weekend activities: gorge swim

With thanks to sponsorships from the Australian livestock industries:

        Australian Wool Innovation           Meat and Livestock Australia

Animal Animal Breeding Summer Course 2003    Materials

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Introduction

Bayesian modelling and data analysis are becoming a standard part of the statistical toolkit.

The Bayesian approach might be seen as the ‘update of opinion based on data’ or

‘the combination of information from different sources’.

This use of prior or external information to directly inform about unknown parameters of interest

allows a very rich, hierarchical modelling approach that can closely describe complex systems.

While simple Bayesian models can be analysed analytically, most analysis is via Monte Carlo methods

such as Markov chain Monte Carlo. There is a great range of MCMC algorithms available now for Bayesian computation.

Content

This two-day course introduces the practising statistician to Bayesian analysis. The course is strongly practical,

with emphasis on understanding the fundamental concepts, modelling in a Bayesian context, and ‘doing’ Bayesian analysis.

An outline of the course is as follows.

-         What is Bayesian statistics? Combining prior opinion and data

-         Doing Bayesian analysis: Markov chain Monte Carlo

-         Bayesian modelling through BUGS

-         Describing complex models: hierarchical models, mixture models, meta-analysis

-         Analysing complex models using BUGS

-         Model selection: Bayes factors, reversible jump, model averaging

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Armidale Animal Breeding Summer Course 2004

Module A2: 12 and 13 February 2004

Bayesian Analysis: Case studies in QTL Mapping

Lecturer:  Kerrie Mengersen, Queensland University of Technology, Brisbane

Introduction

This course focuses on Bayesian methods for analysing quantitative trait loci (QTL).  

Outline:

-         QTL in outbred pedigrees: a Bayesian approach to linkage mapping

-         Mapping a monogenic trait

-         Genotype sampling in complex pedigrees

-         Investigating MCMC methods for analysis

-         Case study: selective genotyping and Bayesian mixtures

-         Multipoint linkage analysis and Hidden Markov

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 Armidale Animal Breeding Summer Course 2004

Module B: 16 and 17 February 2004

Advanced genome analysis

Lecturer:   Miguel Perez-Enciso, Universitat Autonoma de Barcelona, Spain     

Outline:

-         Advanced methods for QTL analysis: LD mapping, analysis of crosses between outbred populations

            slides

-         Microarray analysis: Basics, Discriminant techniques, Genetical genomics

            slides

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Armidale Animal Breeding Summer Course 2004

Module C:  18 and 19 February 2004

Essential bioinformatics for animal geneticists

Lecturer:   John McEwan, AgResearch, New Zealand

Outline:

-         getting around sequence databases

-         local sequence comparison, BLAST, genomic alignments with EST contigs and mRNA attached.

-         Global comparisons,  Clustalw

-         Assembly,  CAP3: simple EST assembly and annotation

-         SNP detection, cSNP identification, SIFT, 3D identification (example)

-         expression array interpretation (i.e. post analysis interpretation of results, promoter, lexical

        Notes in html       

        SLIDES

        Software used

            alignment spreadsheet

            PAM  spreadsheet 

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