Moore Notes 1 23 13

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Group Call

  • Participants: Tom, Stephen, Katie, Josh, Guillaume, Dongying
  • Guillaume: SFams updating
    • Had issues downloading some genomes
      • Probably due to webserver being down
      • Might always have to do some by hand (e.g., very large genomes)
    • Insertions into db are slow (5 million so far)
      • Tom might have a solution for doing bulk inserts into MySQL
    • Problems with LAST jobs on UCD cluster (too many sequences going through at one time?)
      • Will also run BLAST
    • Got round 2 genomes data with renamed families from Tom
    • Set up github repository for updating code:
  • Stephen: tuncated SFams
    • Due to errors in IMG's gene prediction pipeline?
      • Can this hypothesis be confirmed?
      • Updated genomes might have improved annotations
    • Could also be due to real truncated proteins (e.g., due to frame shifts)
    • Annotate them in some way (merge, clans, notes)
    • Guillaume did an analysis of truncated sequences - cross reference with Stephen
  • Josh: contacted Jack Gilbert
    • He's interested in being involved in beta-diversity niche mapping
    • Wants to set up a time to talk one-on-one
    • Working with earth microbiome data (lots of 16S data)
    • Will ask if he is doing shotgun metagenomic sequencing (e.g., English channel)
  • Tom: read classifier project
    • Software development mostly done
    • Stephen did statistical analysis of performance
    • Starting data analyses
      • Data set of a free living (e.g., marine) community with lots of novel lineages?
      • Tanya Wojcicki at JGI
      • Look at where new genomes are coming from in IMG (mostly GEBA, lost of cyanobacteria)
  • Jonathan: setting up website on Wordpress
  • Katie: speaking about metagenomics at Brilliant Science Cal Acad event this week
  • In person meeting in Davis
    • Audrey will do a doodle poll
  • Moore foundation meetings - Jonathan at one, Katie at other
  • Progress report was submitted and receipt confirmed