Moore Notes 9 3 14

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Group Call

  • Participants: Katie, Jonathan, Tom, Stacia, Sarah, Guillaume, Dongying, Stephen
  • Sfams repository errors
    • Fixed
      • Inconsistently formatted headers
      • Broken links
      • New tarball
    • Does not affect the extended markers in phyloSIFT
    • Tom working on hosting Sfams at OSU
    • Edhar server at UC Davis will likely have disk failures soon
  • Tom and postdoc working on OTU tree method to analyze co-variation
    • If normalize by depths, similar in some ways to TreeOTU
    • Identify sub-clades on tree that are common across samples
      • Core nodes
      • Correlated nodes
    • Ask Steve Kembel if he or his phylogenetic ecology colleagues are working on something similar
    • Could do it with other gene families besides rRNA
  • Shotmap paper progress
    • Tom: software improvements (user interface, installation with checks and configuration file, gene prediction algorithms)
      • Next: Test on a few different systems (OSU, UCSF, Davis, mac desktop), work to reduce storage usage
    • Stephen: will work on testing, has written up simulation results
    • Stacia: L4 analysis draft text (in separate documents), copy edited manuscript, comparison with Gilbert et al, photosynthetic gene module analysis
      • Next: check if similar trends in Figfams, check if disagreements with Gilbert maybe due to classification rate and diversity
    • Patrick: ran metaHIT samples, analyzed output
      • Next: write up
    • Goal: finalized draft by one week from now
    • Journal: PLoS Comp Bio, then PLoS ONE (they transfer the reviews)
    • Post a pre-print
  • Next week: Sarah