Moore Notes 1 12 10

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PI Call: MW, JG, JE, and KP

  • JG: Bill Cresko review - any metagenomics for conservation ecology?
  • Revising grant activities
    • 1.2d: Rephrase along lines of Tom's comments
    • 1.3: Refer to this section in simulations activity
    • 1.4: Josh's work (ranges could fit here) - may not need to reword
    • 2.1: small rewording maybe?
    • 2.2b: Delete
    • 2.2c: modify to be about ecotypes, not genomic x spatial
    • 2.2d: Already being done by Venter people, Aaron's work? Delete?
    • 2.2e: Alex could test if purifying selection is more important than drift? Endemism? Delete?
    • 2.2f: DARPA project might work on this. Tom/Morgan novelty work (1.2) relates to evolvability. OK?
    • 3.1:
      • Collapse b-d into one activity, maybe write so covers null models and sampling
      • Simulations: links to trees, PD, molecular rates
  • Prioritization for bioinformatics projects (Guillaume)
    • Scripts / tools / software
    • Task tracking / management / jobs / working
    • CAMERA: Guillaume will be point man
    • OWW Wiki: update/maintain public page
    • Communication system, e.g. Email list? Online forum? Gmail group?
    • Software packages and locales: shared /bin directory on genbeo
    • Data / databases
      • Josh
        • OTUs - from rRNA - from ocean PCR and metagenomic data
        • OPFs from metagenomic data
      • James
        • OTUs filtered by narrower taxonomic range (e.g. families)
        • OTUs from both metagenomic and additional ocean PCR data
      • Sam
        • Protein families: alignments, trees from metagenomic data for those families
        • Simulations: Generating and analyzing trees from simulated data
      • Tom
        • All vs. all clustering of protein sequences from whole genome data: build the families
      • Dongying
        • Merge families from different phyla: MySQL database of relationships between taxonomy and sequences (map JGI <-> MicrobeDB?)
        • Install HMMER3 in centralized location: Get consensus sequences for HMM profiles to group HMMs/families into clusters
      • Morgan
        • All vs. all BLASTs: Access to many metagenomic data sets with metadata (grab from CAMERA)?
      • Steve
        • Alignments of metagenomic reads to more gene families (using AMPHORA?)
          • For GOS data set
          • Additional marker gene families from Dongying
          • Additional markers for different taxonomic groups (archaea, Actinos, etc.)
      • Action items:
        • Protein family db meeting on Thursday in Davis
        • Guillaume on OTU call Friday