course_information_-_uga_2020
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- | ==== Short course UGA 2020 - Programming and computer algorithms in animal breeding with focus on single-step GBLUP and genomic selection in practice ==== | ||
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- | === EDITED on February 10, 2020 === | ||
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- | :!: Applications are now closed.\\ | ||
- | All applications received after February 8, 2020 will be put on a waiting list with no guaranteed acceptance. | ||
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- | === When === | ||
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- | May 11 - 29, Athens, GA\\ | ||
- | From 9:00am to 5:00pm | ||
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- | === Course Venue === | ||
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- | Department of Animal and Dairy Science\\ | ||
- | 425 River Road, Athens GA 30602\\ | ||
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- | === Week 1.=== | ||
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- | Introduction to programming in Fortran 95/ | ||
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- | /* {{ : | ||
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- | === Week 2.=== | ||
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- | **Monday - Wednesday: | ||
- | - Advanced programming in Fortran 95/2003\\ | ||
- | - Computer algorithms useful in animal breeding\\ | ||
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- | **Thursday - Friday:** \\ | ||
- | - Introduction to BLUPF90 family programs\\ | ||
- | - Associated programs: renumf90, inbupg, | ||
- | - Modeling: | ||
- | - Basic models: single-trait, | ||
- | - Advanced models: random-regression, | ||
- | - Variance components estimation\\ | ||
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- | /* {{ : | ||
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- | \\ | ||
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- | === Week 3. === | ||
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- | /* \\ | ||
- | {{ :gsip.pdf | Bases for Genomic Predictions - Legarra et al. 2018}} \\ | ||
- | \\ */ | ||
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- | **Monday** \\ | ||
- | - Introduction: | ||
- | - Basis of SNP data | ||
- | - Data manipulation and scripts with Unix tools\\ | ||
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- | /* {{ : | ||
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- | {{ : | ||
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- | \\ | ||
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- | **Tuesday** \\ | ||
- | - GBLUP, SNPBLUP, brief Bayesian Methods | ||
- | - GBLUP with dominance | ||
- | - BLUPF90 with user_file\\ | ||
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- | /* {{ : | ||
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- | {{ : | ||
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- | {{ : | ||
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- | \\ | ||
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- | **Wednesday** \\ | ||
- | - ssGBLUP | ||
- | - Genomic Options in Blupf90 | ||
- | - Cross-validation methods \\ | ||
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- | /* {{ : | ||
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- | {{ : | ||
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- | {{ : | ||
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- | {{ :as13.pdf | Answers to exercises - Assignment 13}} \\ */ | ||
- | \\ | ||
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- | **Thursday** \\ | ||
- | - YAMS | ||
- | - SNP effects from ssGBLUP | ||
- | - Strategies for many genotyped animals | ||
- | - Theoretical accuracies | ||
- | - Use of postGSf90 | ||
- | - Real life example of large application of ssGBLUP \\ | ||
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- | /* {{ : | ||
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- | {{ : | ||
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- | {{ : | ||
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- | {{ :as14.pdf | Answers to exercises - Assignment 14}} \\ */ | ||
- | \\ | ||
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- | **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\\ | ||
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- | /* {{ : | ||
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- | {{ : | ||
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- | /* **All Assignments** \\ | ||
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- | === Instructors: | ||
- | Ignacy Misztal, Daniela Lourenco, Shogo Tsuruta, and Yutaka Masuda (UGA) \\ | ||
- | Andres Legarra and Zulma Vitezica (France) \\ | ||
- | Ignacio Aguilar (Uruguay) | ||
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- | === 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. \\ | ||
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- | === 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. | ||
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- | === 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\\ | ||
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- | === Forms of Payment: === | ||
- | Cash, checks (US) or wire transfers \\ | ||
- | We are unable to accept credit card or PayPal payments\\ | ||
- | Download the payment instructions {{ : | ||
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- | === Deadline Application: | ||
- | < | ||
- | Download the {{application_form_2020.pdf |Application Form}} \\ | ||
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- | **To speed up the process, email your application form to Susan Bradley < | ||
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- | **Payment information will be emailed to you as soon as your application is processed** \\ | ||
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- | \\ | ||
- | === Logistics: === | ||
- | The closest airport to Athens is in Atlanta. For transportation to and from the Atlanta airport, see: https:// | ||
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- | === Housing: === | ||
- | Housing at the university dorms will be available. The registration will be open in April: https:// | ||
- | On-campus hotel (Georgia Center) is also an option: https:// | ||
- | An extended stay hotel provides accommodation at ~ $250/week (DO NOT book before reading reviews): https:// | ||
- | Other housing options can be booked through regular booking websites and Airbnb. | ||
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- | === Athens information: | ||
- | See [[http:// | ||
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- | \\ | ||