BLUPF90

Short course UGA 2022 - Programming and computer algorithms in animal breeding with a focus on single-step GBLUP and genomic selection in practice

POSTED on january 20, 2022 || EDITED on january 22, 2022

THE UPDATES ABOUT THE COURSE ARE FINALLY OUT

Please read the instructions carefully because the structure of the course has changed

When

May 16 - June 3, Athens, GA
From 9:00am to 5:00pm

Course Venue

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

Course Structure

The course will last 3 weeks, and the weeks are split into 2 modules

Module A:
week 1 plus Monday through Wednesday of week 2

• Week 1 (5/16 - 5/20)

Introduction to programming in Fortran 95/2003

• Week 2 (5/23 - 5/25), Monday - Wednesday

Advanced programming in Fortran 95/2003
Computer algorithms in animal breeding

Module B:
Thursday and Friday of week 2 plus week 3

• Week 2 (5/26 - 5/27), Thursday - Friday

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

• Week 3 (5/30 - 6/3)

Monday

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

Tuesday

GBLUP, SNPBLUP, brief Bayesian Methods
GBLUP with dominance
BLUPF90 with user_file

Wednesday

ssGBLUP
Genomic Options in Blupf90
Cross-validation methods

Thursday

YAMS
SNP effects from ssGBLUP
Strategies for many genotyped animals
Theoretical accuracies
Use of postGSf90
Real life example of large application of ssGBLUP

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

Instructors:

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

Attendance:

The course can be attended in full or partially. The attendance in Module A is limited to 25 and in Module B is limited to 40 participants.

Prerequisites for Module A:

• Knowledge of mixed models and quantitative genetics;
• Familiarity with Linux /Unix environments;
• Knowledge of programming in any high-level programming language (e.g., Fortran, C, C++, Java, Python) is a strong plus.

Prerequisites for Module B:

• Knowledge of mixed models and quantitative genetics;
• Familiarity with Linux /Unix environments.

Fees:

1 Module:

Graduate student - $500
Academic - $700
Industry - $1200

2 Modules:

Graduate student - $700
Academic - $900
Industry - $1400

Forms of Payment:

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

Payment information will be emailed to you as soon as your application is processed

Deadline Application:

March 4, 2020.
Applications are no longer accepted

If you have any questions, please email Christa Dempsey christa.dempsey@uga.edu

Logistics:

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

Housing:

On-campus hotel (Georgia Center) is also an option: https://www.hotel.uga.edu/
An extended stay hotel provides accommodation for ~$300/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.