Pre-Conference Workshops

Date: 20th November 2016, Sunday


Workshop 1: Application of R in Bioinformatics
Instructor: Dr. Reinhard Simon
Date:20th November 2016, Sunday from 0900 hrs to 1700 hrs

Venue: 212 CF Bentley Conference Center


Workshop 2: Breeding Data Management & Analysis using BMS & VSNi tools
Instructor: Dr. Donghui Ma and Arllet Portugal
Date: 20th November 2016, Sunday from 0900 hrs to 1700 hrs

Venue: 307-The Great Lakes Conference Room


The aims of the course are to provide statisticians or scientists with interest in statistical programming with additional tools to support reproducibility and productivity. As experiments get more complicated both the design and analysis become more challenging. Modularization, documentation, standardization and keeping logs is a key ingredient to address the challenges involved. The course will be based on latest best practices in the R community and will be entirely based on R.


Topics covered
  • Standardized file organization
  • Use of version management tools (git)
  • Use of analytical templates (based on knitr)
  • Use of tests (testthat)
  • Documentation tools (roxygen)
  • Interactive reports


  • Good working knowledge of R
  • Laptop or PC not older than 2 years (Windows, Mac, Ubuntu)
  • Full administrative rights to install tools on the laptop
  • For the training sessions English should be used on the computer
  • Latest versions of R and RStudio


About the instructor
Reinhard Simon is working currently at the International Potato Center (CIP) in Lima. He has an engineering degree in plant production from the University of Paderborn and a Masters degree in Biochemistry and Molecular Biology from the University of Jena, both in Germany. During his first studies he had formal training in programming with applications in statistics; during his second studies he was trained in bioinformatics. After his first studies he worked as a trial engineer in the evaluation of new grass varieties in a small private company in Germany, after that in plant production on a farm in Germany and as a volunteer in seed multiplication in wheat, maize and rice in Nepal. At the end of his second studies he joined CIP for his masters thesis on candidate genes for resistance to late blight of potato. He then worked briefly as a consultant in information management and bioinformatics before joining CIP as a leader of a support unit for research informatics. He currently is focusing again on bioinformatics in a project to develop genomic tools for sweetpotato.
More information can be found here:

The aims of the course is to expose to modern breeding data management tools to breeders and use of modern tools to perform data analysists. In this course participants will be also introduced to next generation VNSi tools for experimental design generation, fitting mixed models and performing complex analysis.


Topics covered
  • Overview of Integrated Breeding Platform (IBP)
  • Breeding Management System (BMS)
  • Field Data collation & archival
  • Tools for Digitalized data collection
  • Block experiment w/wo missing data
  • Incomplete block experiment and α-design
  • Mixed Model and BLUP
  • BLUP with pedigree
  • Multivariate BLUP w/wo pedigree
  • Animal Model and EBV (Estimated Breeding Value)


  • Minimum system requirement: 2 GB RAM, 1 GHz dual core, 250 GB hard disk
  • Recommended system requirement: 4 GB RAM, 1 GHz dual core, 500 GB hard disk
  • Supported Browsers: Internet Explorer 8 and above, Firefox 20 and above, Google Chrome 27 and above
  • Full administrative rights to install tools on the laptop
  • For the training sessions English should be used on the computer