Moore Notes 11 18 08

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Group Call

  • Dec Meeting
    • Kelly on Dec 11th, maybe 10th
    • Social event on evening of 10th
    • Really just our quarterly meeting (with a site visit)
    • Talk about what folks used to work on (~10 min each)
    • Challenges and issues (e.g. with CAMERA)
    • JE will check with Kelly about what we need to include in the meeting
    • Make a list of things? Check with our labs and discuss with PIs only next week
      • e.g. what data types do people want and how to produce them?
  • Green Lab update and questions
    • Steve K: tried running some CAMERA data through AMPHORA
      • how to translate nucleotide to amino acid before running AMPHORA?
      • how to parse AMPHORA output to get a list of OTUs present in each sample?
      • how to build trees from AMPHORA alignments?
    • Reading 1 paper per week together
    • Genetic distance distribution - revisiting
    • Trying to get UC Davis computer accounts
  • Pollard lab update and questions
    • Sam: how to weight branches in a path decomposition?
      • Sourav will send his paper (from masking): for pairs of leaves
      • Sam wants to re-weight leaves, not pairs
      • Sourav will send published work on this (e.g. Waterman et al)
      • Josh: more generally interested in entropy-like axioms (a la economics literature)
      • Steve: Rao's quadratic entropy (Simpson's diversity based)
      • Sam: can the tree be used to embed the species in a vector space (characterize each species by a list of features) and then use entropy? Sourav: some work on distance between trees.
    • Josh: everything is everywhere and the environment selects theory still in favor?
      • Sourav: some what out of favor
      • Jessica: been addressed a lot (will point him to papers), but there is no theory about body-size and community assembly
      • Jessica: maximum entropy literature has been used for species-area, but not for predicting phylogeny or phylogentic diversity