Moore Notes 5 5 10
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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
- JE: Elke (Kepler project lead at UCSD) wants to talk about STAP/workflows
- 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
- JE blog about lack of openness of RDP/Silva alignments http://phylogenomics.blogspot.com/2010/04/yuck-rrna-databases-restrictions-on.html
- 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