MoBPS Cookbook
A Practical Guide to Modular Breeding Program Simulator
Welcome
Welcome to the MoBPS Cookbook - a practical, hands-on guide to using the Modular Breeding Program Simulator!
What is MoBPS?
MoBPS (Modular Breeding Program Simulator) is a powerful R package for stochastic simulation of breeding programs (Pook, Schlather, and Simianer 2020). Whether you’re working with:
- Animal breeding (dairy cattle, pigs, chickens, etc.)
- Plant breeding (maize, wheat, crops with selfing/DH)
- Conservation programs
- Research on breeding strategies
MoBPS provides the flexibility and tools you need to simulate, analyze, and optimize breeding schemes.
About This Cookbook
Unlike traditional reference manuals, this cookbook is designed to:
- ✅ Show you HOW to accomplish specific tasks
- ✅ Provide working examples you can copy and adapt
- ✅ Build progressively from simple to complex scenarios
- ✅ Focus on practical workflows rather than exhaustive parameter lists
Who Should Use This Book?
This cookbook is for:
- Beginners learning MoBPS for the first time
- Practitioners designing breeding programs
- Researchers evaluating breeding strategies
- Students studying quantitative genetics and breeding
How to Use This Book
The book is organized into 5 main parts:
- Getting Started - Installation, core concepts, your first simulation
- Building Populations & Traits - Creating realistic founder populations
- Selection, Mating & Breeding - Simulating breeding programs
- Genotyping & Genomic Analysis - Working with SNP data and predictions
- Advanced Topics & Reference - Expert techniques and function references
Recommended approach: - Start with Part 1 if you’re new to MoBPS - Use Ctrl+F / Search to find specific topics - Run the code examples in your own R session - Modify examples to fit your needs
Getting Help
If you get stuck:
- 📧 Contact Torsten Pook: Torsten.pook@wur.nl
- 🌐 Visit www.mobps.de
- 📦 GitHub repository: github.com/tpook92/MoBPS