BLUPF90

Applications are now closed. All applications received after February 8,2020 will be put on a waiting list with no guaranteed acceptance. === When === May 11 - 29, 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:
- Advanced programming in Fortran 95/2003
- Computer algorithms useful in animal breeding
Thursday - Friday:
- Introduction to BLUPF90 family programs
- Associated programs: renumf90, inbupg,…
- Modeling: - Basic models: single-trait, multiple trait, maternal,…
- Advanced models: random-regression, competition, threshold, censored,…
- Variance components estimation
/* Introduction to blupf90
Introduction to renumf90
Parallel computing with OpenMP
*/
=== Week 3. === /*
Bases for Genomic Predictions - Legarra et al. 2018

*/ Monday
- Introduction: brief history of genomic selection - Basis of SNP data - Data manipulation and scripts with Unix tools
/* The promise of genomics for animal improvement
Bases for genomic prediction
Unix commands and quality control
*/
Tuesday
- GBLUP, SNPBLUP, brief Bayesian Methods - GBLUP with dominance - BLUPF90 with user_file
/* Models for genomic selection
GBLUP and G matrices
Non-additive effects in the genetic evaluation
user_file in blupf90
*/
Wednesday
- ssGBLUP - Genomic Options in Blupf90 - Cross-validation methods
/* single-step GBLUP
Details in ssGBLUP
Risks of forecasting in animal breeding
ssGBLUP in blupf90
Answers to exercises - Assignment 13
*/
Thursday
- YAMS - SNP effects from ssGBLUP - Strategies for many genotyped animals - Theoretical accuracies - Use of postGSf90 - Real life example of large application of ssGBLUP
/* 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
- Simulation of genomic data using QMSim - Dimensionality of genomic information - Analyses of sequence data - Causative variants - When to weight SNPs
/* 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, Daniela Lourenco, Shogo Tsuruta, 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 is a strong plus. === Fees: === 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
=== Forms of Payment: === Cash, checks (US) or wire transfers
We are unable to accept credit card or PayPal payments
=== Deadline Application: === March 2February 8, 2020
Download the Application Form
To speed up the process, email your application form to Susan Bradley susanb@uga.edu
Payment information will be emailed to you as soon as your application is processed

=== 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.