Moore Notes 10 21 08

From OpenWetWare
Jump to navigationJump to search


Home Project People News For Team Calendar Library

PI skype chat (JG, JE, KP)

  • OWW website:
    • Steve still needs to
      • fix calendar
      • Transfer relevant information from Jonathan's wiki over to the openwetware page rather than link out to it
    • Katie will look into photo images from Dennis Kunkel
  • Tutorial
    • Srijak is working on a general framework
  • Computing resources
    • Use UCD Genome Center cluster
    • Buy our own and have UCD manage it (better?)
    • Buy our own and run it ourselves (getting less difficult)
    • Pay for external compute cycles (e.g. from Amazon, CAMERA)
    • JE is looking into details
  • Next quarterly report
    • needs to have sections relating to our goals
    • JE will talk to Kelly about details
  • Genome Biology Paper published (JE's lab)
    • automated tool for identifying and characterizing marker gene families
    • uses comboDb (~10000 complete genomes), moving from flat file to relational db
    • can now get alignments of these marker genes from any metagenomic sample
    • also does phylotyping
    • to do (Dongying): what is an OTU?
      • different for each marker gene
      • did phyla (easier, used a distance-based method)
      • what % ID should be used for each gene? (so that OTU definition is normalized between marker genes)
      • arbitrary definition has some use/meaning and is simple
      • data-adaptive approach (so that marker genes result in similar estimates of parameters of interest)
      • phylogenetic definition (possibly with correction for different rates of evolution in different clades)
  • What data formats will JG and KP labs need?
    • sequence alignments
    • trees
    • metadata - how to link to external data, e.g. CAMERA?
    • relative abundance (need definition of OTU)
    • (genomic) distance matrices (?)
  • Related collaborations (potential)
    • Genographic study collaboration/Genevieve's project
      • cheap 16S to see if there is anything there
      • blood (pathogens) vs. cheek swabs (diversity) - either useful?
    • NIH human microbiome grants
      • funded ones have been announced (e.g. data center with tools - Owen White)