Moore Notes 9 11 12

From OpenWetWare
Jump to navigationJump to search

ISEEM2 Group call for September 4, 2012

  • Participants
    • Guillaume
    • Josh
    • Stephen
    • Tom
    • Jonathan
  • Tom: SFams paper has been resubmitted
  • Guillaume: Available metagenomic projects
    • How broad should this be?
    • We have a lot of 16S stuff will be ignored - this is the majority of projects on the various repositories/portals
    • Some have targeted viral metagenomic data, others have thermal vent data
    • What are we trying to target?
    • Jack Gilbert's data all appears to be 16S. Josh will talk to Jack to see if there is some metagenomic data. Might want to collaborate with them as they may be interested in doing something similiar.
    • JAE: My main criterion is to identify projects with lots of samples that used the same collection ideology and approach. This is why the Earth Microbiome Project would be good, once the data becomes online.
      • Guilluame: GOS and HOT/ALOHA fit the above model
      • Terra project is a 2.5 year long expedition across the globe to collect marine metagenomic samples. No word yet.
    • TJS: probably also want a consistently sampled location in the ocean to make niche modeling easy
    • Josh: some small samples will be good for validating the predictions
    • Guillaume will start downloading, place on edhar for now.
    • JAE: a few different sites sampled well (within small spatial scales) will be important. English channel might be important. Might also look into other watery places, like hotsprings.
    • Josh chatted with Craig Nelson at ESA and will ask if he has any data or will collect any.
    • JAE: IMG/M has some interesting data that might be relevant. Stephen Hallam - marine microbial communities from MOZ in subartic pacific ocean. Might be some available unpublished data that we can use here as well as MG-RAST. We should probably talk to Moore or Samantha and ask them how to prioritize the processing of marine datasets. Might give SFam HMMs to CAMERA and have them classify metagenomic data into SFams. The larger comparative datasets might be better for us to focus on because 1) more people will be interested in them and 2) we can use them for conducting ecological analyses.
      • need to contact Moore foundation and see if we should set up advisory board or at least make it clear that we can help people process data set.
        • better to involve the community and collaborate with them rather than run off with it ourselves.
        • TJS will draft a letter and JAE will ship it off.