Moore Notes 10 21 08

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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)