Moore Notes 11 3 10

Group Call

• GBMF request for information http://www.moore.org/mmi-rfi.aspx
  • think tank approach, new collaborations will be made later in process
  • separate, linked proposals

• HOT/ALOHA PD paper
  • 6 mo review process, rejected by PLoS Bio
    • JE: academic editors are faster than the professional editors at PLoS Bio
  • Comments from reviewers:
    • Did not like HOT/ALOHA
    • Compare to MEGAN, make it a methods paper, simulations, etc
  • Could roll over to PLoS CB
    • How much do we need to revise?
    • Could add GOS data set
    • Could make it more of a methods comparison paper, e.g.
      • phylOTU - but also want to compare to existing methods
      • DARPA curated analysis: rRNA data from GOS to look at
        • Gerstein paper cites a paper as a source of the rRNA based taxonomy from the GOS samples
          • Paper is here http://aem.asm.org/cgi/content/full/75/7/2221?ijkey=ab55255e066384cfa8e5591352b0d770f0c56edf
          • Supplemental data is here http://aem.asm.org/cgi/content/full/75/7/2221/DC1
          • rRNA classification is here http://aem.asm.org/content/vol75/issue7/images/data/2221/DC1/Table_S3.zip
      • ESPRIT for alpha diversity - only on full length/PCR samples
      • UNIFRAC for beta diversity
      • MEGAN - discuss why not comparable, or try to do a comparison
        • MEGAN DB has results from prior studies including GOS http://www.megan-db.org/megan-db/
      • functional protein analysis (Morgan's PFAM work) - maybe a separate paper
    • more potentially relevant papers:
      • http://www.eurekalert.org/images/release_graphics/pdf/1-Doolittle.pdf
      • http://www.nature.com/ismej/journal/v2/n10/full/ismej200869a.html

• phylOTU resubmission
  • bug fixed
  • new simulation analyses done
    • SILVA simulations
      • more divergent from reference library
      • more reads
      • accuracy is still pretty good - threshold for optimized performance is 0.15
  • GOS reanalysis is almost done
  • manuscript will be done by next Monday - resubmit by next Friday (got extension)

• AMPHORA2 and OPF db/read classifier
  • AMPHORA2 will meet outcomes from original proposal by making a gene family tool for more families
    • Donying's additional markers
    • Eukaryotes
    • Viruses - coordinate with Peter Skewes-Cox in DeRisi lab
  • Other modules for read classification and OPFs
  • glocal alignment issues in HMMR3

• niche-mapping paper
  • Josh wrote up methods - document sent by email
    • Environmental layers carefully chosen
    • Dealt with sampling bias issue
    • MESS plots: Figure 1 shows that our data set does a good job of covering the global environments
  • Bootstrap values from RDP - what cutoff to use for a taxon call?
    • RDP gives a designation across hierarchy of taxa with bootstrap scores
    • Known sequences get bootstrap values in 90-100% range
    • Shotgun sequences from Rebecca's HMP analysis is bimodal with dip at 80% and peaks at 70% and 95%
    • Steve: 50% cutoff down to genus level in Claesson et al.
    • Should look at how results depend on changing cutoff and/or taxonomic level used
  • JG: diversity gradients at different taxonomic levels in literature - will send papers
  • Dividing up writing - separate call to plan