Project Management: Difference between revisions
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Contacted Craig about skype call soon. | Contacted Craig about skype call soon. | ||
==Protein family stuff== | ==Protein family stuff with Steve== | ||
*share dropbox | |||
Starting with PFAM counts across all GOS samples | Starting with PFAM counts across all GOS samples | ||
*Looking at samples | *Looking at samples |
Revision as of 16:51, 21 January 2011
Halophiles
Erin and Andrew getting ortholog sets all halophile genomes Need to make list of things to be done for roche genome paper.
- Re-do crispr analysis for new NCBI genomes.
Darpa
Getting taxon counts from Steve using essentially Amphora 2 pipeline
Manuscripts
- Association paper showing Miguel and Xingpeng methods. Led by Miguel & Xingpeng
- Microbial geographical paper incorporating environment and location. Is it distance or habitat? Using GOS data. Unknown genes? Xingpeng & Morgan
- Unknown genes?
Erebus
Contacted Craig about skype call soon.
Protein family stuff with Steve
- share dropbox
Starting with PFAM counts across all GOS samples
- Looking at samples
- alpha diversity of GOS samples (measure total protein diversity in each sample)
- provide a listing of most diverse samples and indicated if those are environmentally related
- beta diversity of GOS samples (are the samples related...presumbly yes)
- show a tree and possible a network describing the relatedness of the samples
- estimate total number of different protein families for each sample and all samples combined using chao index?
- alpha diversity of GOS samples (measure total protein diversity in each sample)
- Looking at families
- alpha diversity. what fams are the most rich (not that interesting), diverse (interesting and informative)
- provide list of most diverse families and maybe suggest why those are so diverse?
- beta diversity -> do the groupings tell us anything (e.g. are they similar function, similar localization, etc.)
- map to GO terms to see if similar function
- chao index
- estimate total number of proteins for each family in the ocean (what is the most prevalent)
- alpha diversity. what fams are the most rich (not that interesting), diverse (interesting and informative)
Collaboration with Steve would be a comparison between diversity measurements using taxon vs phylogenetic vs functional