Moore Notes 9 10 14

Group Call

• Participants: Katie, Tom, Jonathan, Guillaume, Dongying, Sarah, Patrick, Josh, Stephen

• Call time for Fall
  • Katie and Tom are teaching
  • Mondays 1:30pm starting Oct 6

• Stephen: species level diversity using metagenomic data
  • Gold standards for how to define a species?
    • Average nucleotide identity (ANI) methods don't agree with each other
    • Marker genes (rRNA OTUs at some identity cutoff, e.g., 97%)
    • Taxonomic names (microscopy)
  • Papers
    • John Taylor wrote a paper introducing the idea of phylogenetic species concept based on sequence data
    • Jim Staley wrote a similar paper for bacteria
    • Nikos also working on this
    • http://www.mendeley.com/groups/1359493/number-of-species-of-bacteria-and-archaea/
    • http://www.annualreviews.org/doi/abs/10.1146/annurev-statistics-022513-115654
    • http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00122.x/full
    • http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2010.04964.x/full
    • http://www.ncbi.nlm.nih.gov/pubmed/11118132

• Shotmap paper updates
  • Tom: shotmap code development done, also auto-install and auto-configuration, wrapping up testing on multiple machines
    • Patrick can try desktop
    • Guillaume is getting some perl installation failures, will send logs to Tom
  • L4 data analysis
    • a minority of gene families in photosynthesis module follow Gilbert pattern
    • some diversity metrics agree, but not all
    • better to compare figfams to theirs (KOs really different)
  • MetaHIT
    • Patrick working on text and a figure or two (e.g., identified biomarkers across samples)
  • Analysis results written up by Friday if possible