Dec09 Annual plan

Planning for Annual Meeting (Dec 2009)

• Organization of Sessions:
  • 1 hour per session (maybe longer for shared sessions)
  • 10 minute introduction
  • 40 minutes structured conversation, based on your goals and what kind of feedback/input you want
  • 10 minutes at end to discuss technical issues and other needs (code, data, etc)
• Session Topics:
  • Josh
    • Perhaps partner with Sam, James, Steve, Tom, and others who are interested in the following sessions:
    • Inferring the shapes of microbe ranges from metagenomic distance-decay data
    • Models of community assembly with respect to phylogeny
    • Diversity quantification/estimation
    • OTU classification
  • Sam (while Martin is there, e.g. 9-10 Tuesday)
    • Discussion of results so far of simulations and analysis, and implications for projects using phylogenetic analyses of metagenomic data (Tom, Josh, Steve, me, etc.).
    • Next steps: using phylogenetic analyses of metagenomic reads classified into Tom's protein families, as well as the AMPHORA families, to make inferences about interesting evolutionary rate variation across the trees and/or across environments for specific families? More detailed consideration about what we think is possible and interesting. Would be useful to discuss with people who have dealt with GOS and other real (rather than simulated) metagenomic data.
  • Martin & Alex
    • ZORRO, masking and improving AMPHORA (with Jonathan and Dongying's session)
    • OTUs (adjusting for copy number) (in OTU session)
    • Alex's previous work on ecotypes
  • Tom & Morgan
    • Current consideration: Classification of metagenomic reads into protein families
    • Morgan
      • identification,clustering, and ranking (size, evenness, phylogenetic disribution, pathogenicity, etc.) of genes with unknown function in completed genomes and then in metagenomic samples.
      • discussing non-sequence similarity methods (phylogenetic profiling, neighbouring genes, structure similarity, etc.) for determining the function of these unknown genes
  • Steve
    • Phylogenetic diversity from metagenomic data using AMPHORA genes
      • Talk about GOS analyses - methods to measure phylogenetic diversity
      • Talk about future directions - add other data sets, other gene families, compare with taxonomic diversity
    • Comparing phylogenies from different gene families
      • Compare 16S and AMPHORA phylogenies for reference sequences
      • Measure phylogenetic signal in 16S copy number
      • With Jonathan, Martin, Dongying, others?
  • James
    • Current topic: OTU classification and comparison with neutral, spatially-explicit predictions for (taxonomic) biodiversity.
    • In terms of the objective of quantifying taxonomic diversity, perhaps would make sense to partner with Josh (perhaps also Tom, Steve, Sam, others who have been working on OTU classification)
  • Dongying and Jonathan
    • Protein family metrics from genomes
    • Comparing trees
  • Group session on OTUs
  • Group session on ecological null models
  • Aaron
    • Phylogenetic cobinning for joint inference of linkage and taxonomic diversity in metagenomic read datasets
      • Here I would describe a bayesian phylogenetic model for taxonomic abundance and methods to perform inference under that model project
      • [powerpoint slides]
  • Bioinformatics
    • tracking jobs
    • possible projects/tasks
  • PIs will meet with Kelly for an hour or two
    • no-cost extension
    • grant outcomes
    • CAMERA