Moore Notes 9 10 14
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Group Call
- Participants: Katie, Tom, Jonathan, Guillaume, Dongying, Sarah, Patrick, Josh, Stephen
- Call time for Fall
- Katie and Tom are teaching
- Mondays 1:30pm starting Oct 6
- Stephen: species level diversity using metagenomic data
- Gold standards for how to define a species?
- Average nucleotide identity (ANI) methods don't agree with each other
- Marker genes (rRNA OTUs at some identity cutoff, e.g., 97%)
- Taxonomic names (microscopy)
- Papers
- John Taylor wrote a paper introducing the idea of phylogenetic species concept based on sequence data
- Jim Staley wrote a similar paper for bacteria
- Nikos also working on this
- http://www.mendeley.com/groups/1359493/number-of-species-of-bacteria-and-archaea/
- http://www.annualreviews.org/doi/abs/10.1146/annurev-statistics-022513-115654
- http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00122.x/full
- http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2010.04964.x/full
- http://www.ncbi.nlm.nih.gov/pubmed/11118132
- Gold standards for how to define a species?
- Shotmap paper updates
- Tom: shotmap code development done, also auto-install and auto-configuration, wrapping up testing on multiple machines
- Patrick can try desktop
- Guillaume is getting some perl installation failures, will send logs to Tom
- L4 data analysis
- a minority of gene families in photosynthesis module follow Gilbert pattern
- some diversity metrics agree, but not all
- better to compare figfams to theirs (KOs really different)
- MetaHIT
- Patrick working on text and a figure or two (e.g., identified biomarkers across samples)
- Analysis results written up by Friday if possible
- Tom: shotmap code development done, also auto-install and auto-configuration, wrapping up testing on multiple machines