{ "metadata": { "kernelspec": { "display_name": "Julia 0.3.7", "language": "julia", "name": "julia 0.3" }, "language": "Julia", "language_info": { "name": "julia", "version": "0.3.7" }, "name": "", "signature": "sha256:f11a81b8dd44c8bbc74191a723eeef36176a667de2a42067f0b567df755f14a6" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "##Course 2 <><>\n", "\n", "###Design of Breeding Programs with Genomic Selection\n", "\n", "###May 18-22, 2015\n", "\n", "###Course Instructor:\n", "* Julius van der Werf\n", "* Jack Dekkers\n", "\n", "###Topics Covered:\n", "* Factors affecting and prediction of single and multi-trait response to selection\n", "*\tIncorporating genomic information in response predictions.\n", "*\tInbreeding with and without genomic information.\n", "*\tDesign of breeding programs to exploit the use of genomic information, including the design of phenotyping strategies.\n", "\n", "* [Overview](WebProgram Iowa2015.docx)\n", "\n", "\n", "###Prerequisites: \n", "* Graduate-level course in quantitative genetics.\n", "* Graduate-level course in statistics." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Materials:\n", "#### Notes:" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Day 1:\n", "\n", " * Notes\n", " * [Selection Notes](day1/Notes/Selection_notes.pdf)\n", " * [Building Blocks R](day1/Notes/Day 1a Building Blocks R.pdf)\n", " \n", " * Slides\n", " * [Building Blocks of Quantitative Genetics](day1/Slides/Day1aBuildingBlocks.pdf)\n", " * [Improving Selection Accuracy, BLUP selection](day1/Slides/Day1bEBVacc.pdf)\n", " * [Selection Theory 1: Change of mean](day1/Slides/Day1cSelectionResp.pdf)\n", " * [Selection Theory 2: Change of variance](day1/Slides/Day1dVariance.pdf)\n", " * Exercises\n", " * [Exercise Instructions - Day 1](day1/Exercises/Day1Exercises.pdf)\n", " * [Day 1 Answers](day1/Exercises/Day1Exercises_answers.pdf)\n", " * [Exercise 2.1/3.1 Answers](day1/Exercises/Exercise 2.1_3.1_answers_1.xlsx)\n", " * [2.2 Answers](day1/Exercises/Response_across_age groups_2.2_Answers.xls)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Day 2:\n", "\n", " * Notes\n", " * [MT Selection](Day2/Notes/Day2a MT Selection.pdf)\n", " * [MT Indexes Multistage Selection](Day2/Notes/Day2b MT indexes Multistage selection.pdf)\n", " * Slides\n", " * [Multiple Trait Selection](Day2/Slides/Day2aMulti Trait.pdf)\n", " * [Two-Stage Selection](Day2/Slides/Day2bMultipleStageSelection.pdf)\n", " * Exercise\n", " * [Exercise Instructions - Day 2](Day2/Exercises/Day2Exercises.pdf)\n", " * [2-stage selection example](Day2/Exercises/2-stage Selection_example.xls)\n", " * [Pig 2-stage (Right click, \"save link as\" to download)](Day2/Exercises/Pig-2stage_ex.d2s)\n", " * [Example](Day2/Exercises/Example_5.dot)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Day 3:\n", "\n", " * Notes\n", " * [Overview of Breeding Programs](Day3/Notes/Day3a Overview of breeding programs_FINAL.pdf)\n", " * [Inbreeding Notes](Day3/Notes/Day3b Inbreeding_notes.pdf)\n", " * [BPDesign](Day3/Notes/Day3c BPDesign.pdf)\n", " * [Cost Benefit](Day3/Notes/Day3e CostBenefitBrPro.pdf)\n", " * [Market Share](Day3/Notes/Day 3f Marketshare.pdf)\n", " * Slides\n", " * [Design of Breeding programs \u2013 overview](Day3/Slides/Day3aDesignofBP.pdf)\n", " * [Inbreeding](Day3/Slides/Day3b Inbreeding.pdf) \n", " * [Optimal Contribution Selection](Day3/Slides/Day3cOCS.pdf)\n", " * [Optimizing Breeding Program Design](Day3/Slides/Day3dOptBP.pdf)\n", " * [Economic Evaluation of breeding programs](Day3/Slides/Day3eEvaluationBP.pdf)\n", " * [Cost Benefit analysis in competitive markets](Day3/Slides/Day3f Marketshare.pdf)\n", " * Exercise\n", " * [Exercise Instructions - Day 3](Day3/Exercises/Day3Exercises.pdf)\n", " * [Inbreeding Prediction (Right click, \"save link as\" to download)](Day3/Exercises/Day 3Inbreeding prediction.d1s)\n", " * [Day 3 Answers](Day3/Exercises/Day 3 exercises_answers.pdf)\n", " * [Gene Flow](Day3/Exercises/GeneflowanddGv2.xlsx)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Day 4:\n", "\n", " * Notes\n", " * [MAS GEBV index](Day4/Notes/Day4a MAS-GEBV index notes.pdf)\n", " * [Genomic Control of Inbreeding](Day4/Notes/Day4b Genomic Control of Inbreeding.pdf)\n", " * Slides\n", " * [Accuracy of genomic prediction](Day4/Slides/Day4aAccurcayofGP.pdf)\n", " * [GBVs in Genetic Evaluation](Day4/Slides/Day4b GS selection index.pdf)\n", " * [Genomic control of Inbreeding](Day4/Slides/Day4cGenomicControlInbreeding.pdf)\n", " * [Genomic selection in crossbreeding programs](Day4/Slides/Day4d crosbreeding.pdf)\n", " * Exercise\n", " * [Exercise Instructions - Day 4](Day4/Exercises/Day4Exercises.pdf)\n", " * [Day4 Multi Trait GS (Right click, \"save link as\" to download)](Day4/Exercises/Day 4 Multi trait GS.d1s)\n", " * [Day4 Single Trait GS (Right click, \"save link as\" to download)](Day4/Exercises/Day 4 Single trait GS.d1s)\n", " * [Day 4 Answers](Day4/Exercises/Day 4 exercises_answers.pdf)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Day 5:\n", "\n", " * Notes\n", " * [Design of Sheep Population](Day5/Notes/Day5f Design of a sheepreference population for GS.pdf)\n", " * Slides\n", " * [Cost-benefit of genomics in breeding programs](Day5/Slides/Day5aCostBenefitGS.pdf)\n", " * [Design of reference populations](Day5/Slides/Day5bDesignofRefPop.pdf)\n", " * [Imputation](Day5/Slides/Day5c Imputation pdf.pdf)\n", " * [Dairy](Day5/Slides/Day5d Dairy.pdf)\n", " * [Beef](Day5/Slides/Day5e Beef.pdf)\n", " * [Pigs](Day5/Slides/Day5e pigs.pdf)\n", " * [Poultry (DO NOT USE FIREFOX TO OPEN. MAY CRASH)](Day5/Slides/Day5f Poultry.pdf)\n", " * [Sheep](Day5/Slides/Day5cGSinSheep.pdf)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Spreadsheets for Course\n", "[Spreadsheets](BPW2015_Spreadsheets.ipynb)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Software for Course <><>\n", "[SelAction](http://www.wageningenur.nl/en/Expertise-Services/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genetics-Group/Research/Software.htm)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "[A few BBQ photos!](BBQ.ipynb)" ] } ], "metadata": {} } ] }