Moore Notes 10 9 13

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Group Call

  • Participants: Katie, Jonathan, Guillaume, Ladan, Sarah, Stephen, Josh, Patrick
  • IMG cron job to update databases
    • No API for getting IMG genomes downloaded
    • Jonathan will contact Nikos
  • Guillaume: PICRUSTs
    • Successful result running it on one sample
    • Tom will run the metagenomes associated with the same samples using the same annotation tool
      • Compare to assess how well PICRUSTs maps 16S to proteins
  • Patrick: MetaCyc
    • Formatting MetaCyc so that it can be used with ShotMap to annotate metagenomes
    • Simulations to see how it performs
      • Families are very partitioned, so worried about misclassification
      • Has good precision with sequences in MetaCyc
      • Will next look at genomes from BioCyc that aren't in MetaCyc for external validation
    • Jonathan: need to check the phylogenetic diversity of the genomes
    • Stephen: don't need high coverage for precision-recall, but maybe for other performance measures
    • Stephen: check out minpath for prediction of pathways from enzymes
      • Patrick: wants to start with smallest pathway unit (1-1 or 1-small number)
  • Josh: working on Jack Gilbert's Gulf of Mexico sediment study
    • Rasters of sea floor metadata