Moore Notes 9 10 08

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Full Group Conference Call (PIs plus lab members)

  • Update on Kepler work flow meeting with UCD and CAMERA
    • CAMERA is already working with Forest Rohwer
    • Our tools would be a second project, using Amber Hartman's rRNA work flow as a test case
    • CAMERA will support conversion of our algorithms/documentation into CAMERA
  • Sean Eddy has been working on an Infernal RNA alignment tool
    • rRNA alignment algorithms are better now (options that work well for this)
    • Scanning DNA with protein family HMMs is getting better/faster (good for metagenomics)
  • James and Liz Arrowhead meeting poster update
    • What ecological patterns can/should we look for with metagenomic data?
  1. Geographic distance decay with libraries of reads and environmental variables (GOS open ocean data)
  2. Analysis of Rusch library to library distance (arbitrary % overlap cutoff, other similarity measures)
  3. What ecological theory might inform choice of metric, and its expected distribution (neutral theory)?
  4. Metagenomic "genomic" distance (vs. whole genomes or library distance), issues: sampling, withing vs. between genomes, 
     read depths, alignment
  * Simulations are needed (with genomic component, evolution)
  • Dongying update on gene family analysis
    • evenness index
    • universality index
    • output: set of gene families for metagenomic analysis (profiles, trees)
  • Openwetware website
    • try to hire Steve Green to get it up