Moore Notes 1 12 10

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