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| ==Halophiles==
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| Erin and Andrew getting ortholog sets all halophile genomes
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| Need to make list of things to be done for roche genome paper.
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| #Re-do crispr analysis for new NCBI genomes.
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| ==Darpa==
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| Getting taxon counts from Steve using essentially Amphora 2 pipeline
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| ===Manuscripts===
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| #Association paper showing Miguel and Xingpeng methods. Led by Miguel & Xingpeng
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| #Microbial geographical paper incorporating environment and location. Is it distance or habitat? Using GOS data. Unknown genes? Xingpeng & Morgan
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| #Unknown genes?
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| ==Erebus==
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| Got 3 samples shared on mg rast. Need to run them through pfam pipeline.
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| ==Protein family stuff with Steve==
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| *share dropbox
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| Starting with PFAM counts across all GOS samples
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| *Looking at samples
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| **alpha diversity of GOS samples (measure total protein diversity in each sample)
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| ***provide a listing of most diverse samples and indicated if those are environmentally related
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| **beta diversity of GOS samples (are the samples related...presumbly yes)
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| ***show a tree and possible a network describing the relatedness of the samples
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| **estimate total number of different protein families for each sample and all samples combined using chao index?
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| *Looking at families
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| **alpha diversity. what fams are the most rich (not that interesting), diverse (interesting and informative)
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| ***provide list of most diverse families and maybe suggest why those are so diverse?
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| **beta diversity -> do the groupings tell us anything (e.g. are they similar function, similar localization, etc.)
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| ***map to GO terms to see if similar function
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| **chao index
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| ***estimate total number of proteins for each family in the ocean (what is the most prevalent)
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| Collaboration with Steve would be a comparison between diversity measurements using taxon vs phylogenetic vs functional
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