Moore Notes 5 5 10

Group Call

• No-cost extension
  • KP: email Gail/Lauren to get estimates
  • JE: UCD Chancellor is working on admin efficacy

• CAMERA
  • JE: Elke (Kepler project lead at UCSD) wants to talk about STAP/workflows
    • will check on AMPHORA, ZORRO
    • future developments: OTU pipeline
  • KP: we will be able to revise CAMERA outcomes with Kelly

• Open microbiome initiative (Rob Knight with Owen White, Pat Floss, et al) http://qiime.sourceforge.net/
  • JE blog about lack of openness of RDP/Silva alignments http://phylogenomics.blogspot.com/2010/04/yuck-rrna-databases-restrictions-on.html
    • used in Greengenes, STAP, etc.
    • Sean Eddy's lab is thinking about redoing all these alignments and hosting them openly
  • Software, e.g. Unifrac (PyCogent: http://sourceforge.net/projects/pycogent/)
  • Mostly human microbiome project
  • Linked to Built Environment program?
  • Morgan: BioTorrents works to just get data out there, but isn't an organized Db

• Aram (Pollard lab rotation student) made a webscraper to grab data from CAMERA
  • Tom: Same directory configuration at CAMERA
  • Put on Edhar? Getting full though...
  • Tom will figure out size of the data sets

• OTU paper
  • Outline: http://iseem.private.openwetware.org/wiki/Paper_16S_Based_OTU_Identification_Pipeline
  • Give Tom feedback this week
  • Draft of methods and results in 2 weeks
  • Draft of other sections in 4 weeks
  • Submit in 6-8 weeks

• Distance-decay theory vs. data available
  • JG: GOS plots from James and Josh at annual meeting show no distance-decay pattern
  • Steve's 16S data shows really course differences in habitat are main drivers
  • James' work treats environment as fixed, works in space - so this is a problem
  • New data? e.g. JG's PCR-based soil data
  • New theory for environmental gradients?
  • KP: Data will change, Moore wants to fund theory-driven data collection
  • Write review about sampling?
  • JG: Can we communicate about data sets as we produce them?
  • Morgan: Can we work on CAMERA? Tom: schema changes, not flat files