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course_information_-_uga_2020

Short course UGA 2020 - Programming and computer algorithms in animal breeding with focus on single-step GBLUP and genomic selection in practice

EDITED on February 10, 2020

:!: 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

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


Week 3.

Monday

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


Tuesday

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


Wednesday

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


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


Friday. Single-step without limits and practical issues

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



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
Download the payment instructions here
If paying by wire transfer, the information is here

Deadline Application:

March 2, February 8, 2020, Applications closed: we will put the new applications (after February 8, 2020) to a waiting list with no guaranteed acceptance.
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:

course_information_-_uga_2020.txt · Last modified: 2020/02/12 22:01 by dani