Moore Notes 1 21 09

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Group Call 1/21/09

  • Annual Report
    • Kelly sent a template (simpler if we don't use it - will if there is time)
    • Be sure to include:
      • Any collaborations with people outside project
      • Text for meeting objectives (outline is on the wiki)
      • Figures and draft/published papers
    • Budget: Gail/Jonathan
  • Datasets / Back translation problem
    • Martin has scripts for back translation
    • Discussed what AMPHORA does (e.g. masked vs. not)
    • SQL db
    • UCD accounts (bobcat, genbeo)
  • Simulations
    • MetaSim
      • pretty easy to use
      • might have to do some scripting to generate input files in a high-throughput way
      • what is effect of clone length with 454 simulations? Sam will look into this
      • main issue is closed source (probably OK)
    • ROSE
      • Maritn thinks the models are not realistic (single rate on the tree?)
  • Trees
    • long list of possible methods (Brenner lab, Bioinformatics paper, Morgan Price, supertree, supermatrix)
    • Aaron will get paper from Davis folks
  • BioPerl
    • Srijak working on using BioPerl to run AMPHORA on Macs