ibp simulation tools workshop wageningen, june 2 nd 2011 1 simulation tools – workshop4 report
TRANSCRIPT
IBP Simulation Tools WorkshopWageningen, June 2nd 2011
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Simulation Tools – Workshop4 Report
Structure of Workshop
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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?
Summary of Responses
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Use-friendly
Intuitive
Functional
Suitable
Recommend Use
0 10 20 30 40 50 60 70 80 90 100
NOYES
Proportion of responses (N = 16; Blank =“NO”)
Comments from participantsBest Features
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“Ability to simulate and estimate different population requirements 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 participantsBest Features
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“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”
Comments from participantsWeakness
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“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”
Comments from participantsOther comments
7
“A very promising tool, however time allotted for this workshop was 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
9
Familiar Windows-like environment, graphics and links to pipeline
BUT complex and not-necessarily intuitive
Usability
10
Most participants recognized that simulation:Enhance understanding of GE system and programCan evaluate multiple optionsImprove efficiency of breeding programsAnd tools had significant and powerful functionality
However:Complex inputs make difficult to specify simulationsImproved tools are required to document breeding
strategiesComputing power maybe limitation
Other comments
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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
Future…
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Integration with GenStat output via FlapJack currently allows importation 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 simulationsLinkage with costs to evaluate strategies both in terms of
genetic gain and costWork with Use-Cases to apply simulation tools to answer
strategic and tactical questions about design and implementation of breeding programs.
Roles of simulation team
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Undertake ‘strategic’ simulation analysese.g. Assessing potential of marker-assisted
selection in different types of trait, gene, environment systems
Provide service to use case scientistsPut results of QTL analyses into a simulation formatHelp use-case scientists to design and evaluate
options forDesign 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