First workshop on simulation of breeding programs with MoBPS

MoBPS is a software for the stochastic simulation of breeding programs that has recently been adopted by Wageningen University & Research (WUR) as Torsten Pook, the main developer of the tool, joined Wageningen recently and will continue the development of the framework partly within the Breed4Food project. 25 highly motivated participants from animal, plant and aqua breeding joined the workshop, including several international participants and people working in research and industry.

Getting started with MoBPS

The workshop provided a general introduction to the design of breeding programs, their simulations, and the specific use of the software MoBPS. The main focus was on exercise sessions, true to the motto: “You only learn programming by doing it.” The first day focused on the web-based user interface of MoBPS (available at www.mobps.de) that guides users through the steps of designing a breeding scheme, culminating in a flash environment, where a breeding scheme can be drawn as a combination of nodes (groups of individuals) and edges (breeding actions).

Sophisticated simulations with the R-package

In the second half of the workshop, the R-package of MoBPS was used directly. As the R-Package can be computationally more efficient and generally provide more flexibility, more sophisticated simulations should be performed with the R-package itself, whereas the interface should be mostly seen as a tool for people with limited programming knowledge or help to get started with the framework. Exercises included an introduction to the individual steps of a simulation study like setting up a founder population and traits, performing a breeding value estimation, and setting up simulations with multiple breeding cycles. These were then pierced together to simulate various breeding schemes in sheep, dairy cattle, and maize. “With more than 300 parameters in the main function of MoBPS and 120 pages of user guidelines, getting started with MoBPS can be quite challenging,” says Torsten Pook. “It is mostly about learning how to find the few parameters that you actually need for your simulations.”

To make the workshop more accessible to international attendees and thus spread the word about the software that is being developed at WUR, WIAS is planning an online version of the workshop in the near future. The plan is that this workshop will be hosted and updated annually. All the course material is freely available at http://github.com/tpook92/MoBPS.