BLUPF90

Applications are closed.

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

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

Introduction to programming in Fortran 95/2003

Computational Techniques in Animal Breeding - Notes

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

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

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

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.

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.

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

• Industry - $1200
  
• Academic - $700
  
• Graduate student - $500
  
• Graduate students from USA who are part of AG*IDEA institution - might be able to waive the registration fee
  
• Prospective graduate students please contact Daniela Lourenco (danilino@uga.edu)

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

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

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

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.

See the official website or separate pages.