Moore Notes 9 3 14

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