Moore Notes 1 8 14

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Group Call

  • Participants: Jonathan, Katie, Tom, Josh, Patrick, Stephen, Ladan, Guillaume
  • Any news on Tara Oceans data?
    • Some data sets in NCBI, but not recently released and not too many locations
    • Tara group did send a query to PLoS Biology about publishing an overview paper (no data in that paper, so said they were submitting data papers elsewhere)
  • EFI:
    • Katie talked with John Gerlt (Director) and Matt Jacobson (PI)
    • They are interested in our novel and unannotated gene families:
      • SFams with no PFAM annotation, good QC, and >1 sequence (Tom: maybe focus on groups of sequence similar SFams)
      • Microbiome assemblies
    • Blue waters compute time
      • All-vs-all BLAST
      • Adding metagenomes to SFams
    • JE: more novel functions outside human micro biome
      • Patrick: Bacteriodetes has particularly low level of annotation
  • Shattuck data storage: server is getting full
    • Intermediate data generated by shot map is huge
      • Some things could be deleted (can easily regenerate later if needed), e.g.,
        • Translated reads and output of splitting on stops (only takes an hour to redo this)
        • Rapsearch raw search results
    • Stephen: How to implement?
      • Could write a post-processing script
      • Katie: would be nice to have the post-processing script automatically run be default
    • Tom: What about advanced compression techniques (better than gzip)
      • JE: DNA and other supposed to be somewhat superior (Gale Rosen)
      • Stephen: bzip is better, but slower
  • Guillaume: check on opening ports on shattuck for SFam distribution
  • Jonathan: Not using WordPress website so will delete
  • No call on 1/22. Next week: Maybe Stephen