Moore Notes 6 2 10

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Group Call

  • June meeting plans
    • getting room with projector etc
    • audio recording - laptop
    • chalk or dry erase board (take photos)
    • head count: 4 UCSF, 2 UVA, 4? UCD
    • copy format from last time - set up wiki page
      • add time to discuss manuscripts?
  • Evolution meeting in Portland
    • coordinate travel
  • OTU paper
    • request for comments from authors
    • waiting on results:
      • GOS analysis
      • clustering linkage method comparison (PD vs. PID vs. taxonomy)
  • Josh: oil spill diversity research
    • funding: BP, NSF
    • JE talked to Janet Jansen (LBL/JGI) at ASM about samples collected in gulf
      • probably asked by administration
    • special session on oil spill
  • JE summary of ASM meeting
    • many people producing data sets that have better biogeographical sampling
    • lots of clinical microbiology
    • not much on techniques, technological developments - more about biology
    • did not see anything on new informatics developments or metagenomics
    • lots of 454/Sanger sequencing of 16S rRNA
    • sequencing error is really problematic for ORF finding and SNP finding
    • HMP new genomes - 150 strains, poor quality assemblies (100s of contigs)
      • targeting ~1000 reference genomes and will not be finishing/improving assemblies
      • KP: do we need assemblies for gene family focused analyses?
      • but, contamination problems persist
      • more species does provide better sampling of pan-genome of each strain
      • most do not add a lot of phylogenetic signal
    • Norm Pace: 200 phyla of bacteria
    • Ed DeLong gave several talks
  • CAMERA
    • had good conference call about a month ago
    • they promised to do a Kepler workflow for STAP + WATERS
    • download didn't work, want to test one online
    • no further contact - missed them at ASM (booth in vendor area), haven't gotten back to JE
    • OTU pipeline?
    • alternative projects: MOTHUR, qiime
  • Open access/RDP
  • Unique identifiers for organisms (tracking, even if taxon name changes)