Data Science and Plant Breeding Simulation Workshop

Thursday March 23, 2017

Ben Pomeroy Student/Alumni Learning Center, St. Paul Campus



1:00 - 1:10    Welcome and Introduction

1:10 - 2:00    Karl Broman, Steps Toward Reproducible Research. 

2:00 - 2:10    Break and snacks

2:10 - 3:30    Rex Bernardo, 1st Invitational Pro-Am Plant Breeding Tournament


Our “Computational Tools and Plant Breeding” workshop will focus on different uses of computational resources and methods in plant breeding. This event will feature two sessions: first, a plant breeding simulation competition and second, a workshop on data science and reproducible research best practices. Our two renowned session leaders are Dr. Rex Bernardo (University of Minnesota) and Dr. Karl Broman (University of Wisconsin - Madison). Please be sure to register in advance so we can organize your team for the Pro-Am Invitational.

Session 1: Steps Toward Reproducible Research

Time: 1:10 to 2:00 PM

Leader: Dr. Karl Broman


A minimal standard for data analysis and other scientific computations is that they be reproducible: that the code and data are organized and assembled in a way so that another group can recreate all of the results (e.g., the figures in a paper). Adopting a workflow that will make your results reproducible will ultimately make your life easier; if a problem or question arises somewhere down the line, it will be much easier to correct or explain. But organizing analyses so that they are reproducible is not easy. This workshop will provide an overview of recommended practices, with hands-on activities to help guide participants along a path towards reproducibility.


Session 2: Plant Breeding Pro-Am Invitational

Time: 2:10 PM to 3:30 PM

Leader: Dr. Rex Bernardo


In the 1st Invitational Pro-Am Plant Breeding Tournament, teams will compete to maximize the genetic gains in a simulated breeding program for barley. Each team will include 2-3 graduate students and a professional plant breeder. Together, the teammates will make breeding decisions in an attempt to develop a barley cultivar that meets certain standards for three traits that show unfavorable correlations: grain yield, protein concentration, and disease resistance. Each team will need to decide which parents to cross; how many crosses to make; how many progeny to create in each cross; when and how to use markers in selection; how many locations to use in phenotyping; and which specific progeny to select in each stage--all while staying within a fixed budget. Nice prizes await the winners! Uber-competitive students are especially encouraged to participate.