Moore Notes 1 7 09

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Group Conference Call (skype)

  • UCD Cluster
    • send logins to JE to send to Mike Lewis
    • how should people do analyses (cluster, Eisen lab linux machine bobcat)
  • Srijak is working on data set of protein families
    • alignments w/ metagenomics reads from depth series
    • need to build trees
  • Annual report due in ~3 weeks
    • JG and SK will make a wiki page about what they need (e.g. rRNA alignment/trees for assessing diversity)
    • JE lab will make a page about what datasets are available
    • JGI database? Check in literature for who has already done this?
    • GOS, depth series (e.g. using infernal)
  • Simulations
    • Martin's data is on website
    • metaSim, JGI simulation paper (datasets available, not clear exactly how done)
    • Make a new method
      • Idea: hold out some complete genomes as "complete" and fragment the rest to look like metag. reads
      • What do reads look like: how long (depends on seq technology)? how much overlap (depends on community structure)?
      • supermatrix methods depend a lot on how this is done
      • simulation process should imitate community structure (rel abundances), molecular methods
      • would we do some assembling? better to focus on raw reads
      • should look at a range of parameters
  • Tree-building
    • additional people to talk to: Lior Pachter, Brian Moore
    • supermatrix
    • supertree
      • for combining across gene families? how to map taxa?
    • "traditional" tree building with all data (is this different from supermatrix? maybe just in its use of missing data)
    • Delong paper: phylogenetic analysis on a depth series
  • Planning:
    • Jenna, Steve, Sam will start a wiki page on simulations
    • Sam will email Martin to see if he can chat
    • JG will start a data wish list page