Moore Notes 5 8 13

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Group Call

  • Participants: Katie, Jonathan, Tom, Stephen, Ladan, Guillaume, Dongying
  • JE: Invited to Ed DeLong metagenomics meeting in Catalina (NSF)
  • SFams updater
    • Tom & Guillaume have finished updater code
    • Tim L has done the QC code and functional annotation code
      • No help yet from JGI regarding annotation files
      • So doing our own annotations
    • Job with new genomes (>2000) will be launched in two weeks
    • JE: what about contigs from environmental samples and not just genomes?
      • Tom: talked to C. Titus Brown, who thinks this is possible
      • Would have to modify some of automation workflow (e.g., outside IMG)
      • JE: BAC and cosmid sequences
        • Tom: let's work on this after the current update, e.g., for next paper
      • Tom: what about assembled metagenomic genomes (e.g., IMG MG)?
    • Stephen: need to be cautious about seeding families with truncated sequences
    • KP: Discuss at June 17 meeting
  • Niche mapping of protein functions in soil data (with Jack Gilbert)
    • Continental US samples
    • Tom: If ecologically diverse, should we work on this?
    • Josh will follow up on marine samples
    • Stephen: misclassification could be a problem
    • Tom: more diverse communities means
  • Josh: global diversity estimation
  • June 17 Meeting
    • Logistics
      • Start time? 10am
      • Lunch in
      • End by 5pm
    • Organization of presentations
      • Code: MRC, sims, diversity mapping, simulations, phylogenetic OTUs
      • Data: SFams new release, classification outputs of metagenomes (e.g., English Channel)
      • Analyses: Maps, English Channel results, simulation results, maybe phylogenetic OTUs on genomes
      • Brainstorming sessions on specific topics: SFams new features, merging MRC with PhyloSift, accurate relative abundance of protein families
  • Progress report text due to Katie by May 26th at latest