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
- Steve K: tried running some CAMERA data through AMPHORA
- 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
- Sam: how to weight branches in a path decomposition?
