Moore Notes 10 24 12

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Group Call

  • Participants: Guillaume, Stephen, Josh, Katie
  • Data availability and GBMF collaborations
    • Checked CAMERA?
      • Guillaume will double check
    • What are we looking for specifically?
      • shotgun metagenomic
      • many samples within one experiment
      • many diverse marine environments (with metadata)
      • FASTQ if possible (for quality - not available for GOS)
  • Functional profiles via 16S + genomes
  • Josh - needs the shotgun data and protein families to do functional mapping
    • Meanwhile working on beta diversity of 16S (taxonomic)
    • Also phylogenetic diversity
      • how aggregated vs. dispersed reads are on a tree (Steve Kembel's approach)
      • want to separate out taxonomic signal from the PD map (Forest et al. Nature paper)
    • Literature review to see what people use niche maps for (e.g., identifying hotspots of diversity)
  • Stephen - it would be good to focus on specific gene families
    • Reliable ones, interesting ones
    • For example, proteins that are diverse or abundant in ocean acidification hotspots
  • Guillaume - SFams
    • Cleaning up bug with NCBI IDs vs. IMG IDs
    • Add hit counter for tracking SFams downloads