Moore Notes 9 24 14

Group Call

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

• Interesting papers:
  • http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001889
  • http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014129a.html
    • SAR11 marine diversity patterns validate our predictions (cites our ISME paper)
    • Talks about seasonal diversity as an "emerging paradigm"

• Stephen: has a tool https://github.com/snayfach/SRAtools
  • to download and process data from NCBI SRA
  • converts file types

• Tom: half way through shotmap draft
  • Next to Stephen

• Sarah: Comparing taxonomic and functional diversity in metagenomic samples (slides)
  • Compare gene families of interest to 37 taxonomically informative "elite" families
  • For each pair of samples, compute KR "earth mover's" distance for each family
  • Then look at KR for families of interest vs. KR distributions for elite families
    • What is KR measuring exactly? Does it depend on number of sequences and their abundances?
    • How many samples and how diverse do they need to be? Within vs. between sample diversity? Inter-study variation a problem?
    • Positive controls? Nitrite reduction, glycoside hydrolases
  • How to summarize over all pairwise comparisons? Multiple testing?
  • Visualizations
  • Alternative distance measures

• Future calls
  • Mondays @ 1:30pm starting 10/6
  • Oct 6: tentative shot map call
  • Oct 13: TBD
  • Oct 20: Josh will present on beta diversity and range shapes