Short course UGA 2018 - Programming and computer algorithms in animal breeding with focus on single-step GBLUP and reality of genomic selection

EDITED on May 21st

:!: Applications are closed.

When

May 7 - 25, Athens, GA
From 9:00am to 5:00pm

Course Venue

Department of Animal and Dairy Science
425 River Road, Athens GA 30602

Week 1.

Introduction to programming in Fortran 95/2003

Computational Techniques in Animal Breeding - Notes


Week 2.

Monday - Wednesday:

  1. Advanced programming in Fortran 95/2003
  2. Computer algorithms useful in animal breeding

Thursday - Friday:

  1. Introduction to BLUPF90 family programs
  2. Associated programs: renumf90, inbupg,…
  3. Modeling:
    1. Basic models: single-trait, multiple trait, maternal,…
    2. Advanced models: random-regression, competition, threshold, censored,…
  4. Variance components estimation

Introduction to blupf90

Introduction to renumf90

Parallel computing with OpenMP


Week 3. (Final Program)


Bases for Genomic Predictions - Legarra et al. 2018

Monday

  1. Introduction: brief history of genomic selection
  2. Basis of SNP data
  3. Data manipulation and scripts with Unix tools

The promise of genomics for animal improvement

Bases for genomic prediction

Unix commands and quality control


Tuesday

  1. GBLUP, SNPBLUP, brief Bayesian Methods
  2. GBLUP with dominance
  3. BLUPF90 with user_file

Models for genomic selection

GBLUP and G matrices

Non-additive effects in the genetic evaluation

user_file in blupf90


Wednesday

  1. ssGBLUP
  2. Genomic Options in Blupf90
  3. Cross-validation methods

single-step GBLUP

Details in ssGBLUP

Risks of forecasting in animal breeding

ssGBLUP in blupf90

Answers to exercises - Assignment 13


Thursday

  1. YAMS
  2. SNP effects from ssGBLUP
  3. Strategies for many genotyped animals
  4. Theoretical accuracies
  5. Use of postGSf90
  6. Real life example of large application of ssGBLUP: American Angus

Introduction to postGSf90

How large-scale genomic evaluations are are possible

Theoretical accuracy

Answers to exercises - Assignment 14


Friday. Single-step without limits and practical issues

  1. Simulation of genomic data using QMSim
  2. Causative variants
  3. When to weight SNPs
  4. Dimensionality of genomic information

Data simulation using QMSim

YAMS - A sparse matrix package

Questions in Genomic Selection and History of single-step



All Assignments

Assignments Course 2018



Instructors:

Ignacy Misztal, Shogo Tsuruta, Daniela Lourenco, and Yutaka Masuda (UGA)
Andres Legarra and Zulma Vitezica (France)
Ignacio Aguilar (Uruguay)

Attendance:

The course can be attended in full or partially. The attendance in Weeks 1-2 is limited to 25 and in Week 3 is limited to 35. Those attending for 2-3 weeks will have priority.
Those familiar with basics of Fortran 95 can skip Week 1. Those familiar with the BLUPF90 software can skip Week 2.
Thursday-Friday of Week 2 and Week 3 will involve very limited programming and can thus be attended by those interested in application programs and genomic applications.

Prerequisites:

Participants are expected to be familiar with mixed model equations and quantitative genetics.
Familiarity with Linux / Unix environments a plus.
Knowledge of programming in any programming language a strong plus.

Fees:

The fees will be the same regardless of the number of weeks attended

Forms of Payment:

Cash, checks (US) or wire transfers
We are unable to accept credit card or PayPal payments

Deadline Application:

April 6
Applications are closed
Download the Registration Form

To speed up the process, email your registration form to Susan Bradley susanb@uga.edu

Please mail the registration form and check (made payable to University of Georgia) to:
Susan Bradley
University of Georgia Animal and Dairy Science
425 River Road
Athens, GA 30602 USA

Logistics:

The closest airport to Athens is in Atlanta. For transportation to and from the Atlanta airport, see: https://groometransportation.com/athens/

Housing:

Housing at the university dorms will be available. The registration will be open in April: https://housing.uga.edu/site/register_summer
On-campus hotel (Georgia Center) is also an option: https://www.hotel.uga.edu/
An extended stay hotel provides accommodation at ~ $250/week (DO NOT book before reading reviews): https://www.intownsuites.com/extended-stay-locations/georgia/metro-athens/
Other housing options can be booked through regular booking websites and Airbnb.

Athens information:

See the official website or separate pages.


Group picture