Simulation Tools – Workshop4 Report
IBP Simulation Tools Workshop
Wageningen, June 2nd 2011
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Structure of Workshop
 Roles of simulation team within IBP?
 Brief introduction to plant breeding simulation using the QuGene
platform (this talk)
 Tutorials/examples:
 Phenotypic selection with 1 gene, 1 trait, 1 environment
 Selected examples of simulation applications in breeding program
 Questions?
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Summary of Responses
Recommend Use
Suitable
NO
YES
Functional
Intuitive
Use-friendly
0
3
20
40
60
80
Proportion of responses (N = 16; Blank =“NO”)
100
Comments from participants
Best Features
 “Ability to simulate and estimate different population requirements
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and visualize results graphically. ”
“A very powerful tool … it makes it possible for one to predict the
outcomes of breeding”
“User friendly”
“The tool is great because it allows you to review your breeding
strategy, taking in consideration of critical information from other
research units in the program”
“Integrated with other tools”
“Very robust and flexible”
Comments from participants
Best Features
 “Flexible in the breeding design”
 “Graphics”
 “Best user interface … but not intuitive”
 “Comparing breeding strategies – helps with design for better genetic
gain”
 “Improves understanding of the GE system”
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Comments from participants
Weakness
 “Complex inputs”
 “The learning curve is steep”
 “Additional guides are necessary”
 “Complex”
 “Definition of the breeding program”
 “Requires a better understanding of the breeding procedure”
 “Large number of simulation cycles require more powerful
computers to reduce time”
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Comments from participants
Other comments
 “A very promising tool, however time allotted for this workshop was
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insufficient for good demonstration”
“Go ahead with the breeding program design tool”
“Breeding program design tool looks easier way to build [strategy]
than the text editor”
“Economic integration for good assessment in financial terms”
“Time limitation/constraints for workshop presentation to grasp
procedures ”
“Too much information in a short time”
Summary
Simulations Tools
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Interface
 Familiar Windows-like environment, graphics and links to pipeline
 BUT complex and not-necessarily intuitive
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Usability
 Most participants recognized that simulation:
 Enhance understanding of GE system and program
 Can evaluate multiple options
 Improve efficiency of breeding programs
 And tools had significant and powerful functionality
 However:
 Complex inputs make difficult to specify simulations
 Improved tools are required to document breeding
strategies
 Computing power maybe limitation
10
Other comments
 Insufficient time to adequately cover
material in the workshop
 Links to tools to allow economic evaluation
of breeding strategies would be useful
 Inclusion of templates for standard
breeding methods
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Future…
 Integration with GenStat output via FlapJack currently allows importation
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of much of the information required to specify genetic-environment system
Require better tools to aid description and definition of breeding programs
(may be useful per se)
Development of templates
Explore options for integration with iPlant infrastructure to allow large
simulations
Linkage with costs to evaluate strategies both in terms of genetic gain and
cost
Work with Use-Cases to apply simulation tools to answer strategic and
tactical questions about design and implementation of breeding programs.
Roles of simulation team
 Undertake ‘strategic’ simulation analyses
 e.g. Assessing potential of marker-assisted selection in different types of
trait, gene, environment systems
 Provide service to use case scientists
 Put results of QTL analyses into a simulation format
 Help use-case scientists to design and evaluate options for
 Design of breeding programs (BPDTool)
 Assessing simulation results, given different assumptions about genetic models
controlling ‘unknown’ QTL effects (Excel template and GenStat/FlapJack tools)
 Contacts:
 Adrian Hathorn, Scott Chapman, Jiankang Wang, Mark Dieters
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