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Comment: Migrated to Confluence 4.0


David, Ali, Ali's students, Martha, Liya, Ann


  • Overview of current development status, possible improvement
  • Continuous development of stepwise regression, snp-snp interaction, any bottleneck?
  • Progress of accuracy testing (single marker regression testing), plan for testing more complicated models
  • Getting code running on the new high-end GPU cards in the Lonestar system and exposing it via the Foundation API 


  • The question regarding stepwise regression is how to set appropriate thresholds for getting SNPs in and out. Ann clarified that it is more important to get SNPs in.
    • Ann suggested 0.002 / 1 E-5 for in /out (though Ann is still not clear on why stepwise regression is needed, we might want to just use forward selection for now); stepwise involves computing fit of the whole set of snps
    • Liya suggested empirical values for getting programs to run (make sr workflow works for testing implementation)
    • Liya suggested to consider R/QTL way for handling SR: specifying how many SNPs can get in and how many SNPs can be in the final model
    • Ann suggested Permony for permutation to estimate 'good' threshold
  • Ali will send code to Liya for independent benchmarking and exposing to Foundation API
  • To have DE integration in mind, program needs to take model, thresholds, population structure, maximal number of SNPs, etc. as input options
  • Current approach is good for testing various ways to analyze data