Moore Notes 2 27 13

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Group Call

  • Participants: Katie, Jonathan, Guillaume, Dongying, Josh, Stephen, Tom
  • In person meeting
    • Samantha can't make June 19
    • Move to June 17
    • San Francisco
  • Tom: Needs Dongying's help getting Interpro IDs for IMG genomes
  • Josh: Beta diversity niche mapping
    • Community classification
      • What clustering algorithm? UPGMA seems slightly better than other hierarchical clustering algorithms
      • How many clusters?
    • Not finding distinct clusters - why?
      • Check if find distinct clusters with marine macroorgansim data
      • Bray-Curtis (abundance based) might be flat due to a couple OTUs that dominate - try presence/absence
      • Look at actual Bray-Curtis matrix (ordered by clusters) to confirm no visual patterns
      • Repeat for individual phyla
    • Survey gap analysis
      • Use model to estimate how dissimilar an un-surveyed grid cell is from surveyed locations
      • Points to locations likely to have novel communities
      • Tom: How to validate? Josh: Independent data set, cross-validation; Katie: Collect data
      • Tom: Do they correspond to low certainty locations? Josh: No, not precision. Difference.
      • Sounds cool...
  • Dongying: mutual information based clustering approach
    • Will give update in two weeks
  • New iSEEM2 postdoc starting in April (Sarah Hird)
  • New bioinformatics staff member at Gladstone (Tim Laurant)
  • MMI meeting next week
    • Katie and Russell will be there