Moore Notes 3 20 13

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Group Call

  • Participants: Jonathan, Katie, Stephen, Tom, Josh, Guillaume, Ladon
  • Guillaume: data in CAMERA
    • Found 39 metagenomics projects (15-20 samples per project)
    • Antarctic, coastal, Monterey Bay, ice (marine ice?)
  • Tom/Guillaume: SFams coding session
    • Moving update to UCSF
    • Close to an operational workflow for updates
    • Tim L will perform the QC (precision and recall for new SFams)
    • Keeping up with new genomes pretty well for now, but getting harder
    • Could JGI or someplace else handle future updates?
      • They currently annotate genomes with COGs, PFAMs, InterPro
      • Would need to do the QC and sifting steps
      • Nikos Kyrpides is the person to talk to at JGI
    • Alternative: only process a subset of phylogenetically diverse genomes
  • New structures in SFams
    • Dongying and Nikos' group previously identified novel families that are not easily modeled with known structures (energy minimization)
    • Gave them to structural genome initiative, and they crystalized them
  • Tom: MRC
    • Fully operational
    • Starting to process data for publication
      • Some marine
      • Lots of human micro biome
    • Needs help processing data
    • Setting up a mirror at Davis will also allow us to test how portable the software is
      • Guillaume? In a few weeks
  • Josh: Jack Gilbert NSF proposal
    • NEON field station data (intensively sampled)
    • Biomes
    • Survey gap analysis
    • Estimating total diversity (continental, global)
    • Global seed bank concept
      • American Academy of Microbiology report about the rare biosphere
      • Many other possible explanations