Moore Notes 2 6 13

Group Call

• Participants: Josh, Guillaume, Stephen, Tom, Katie,

• Notify Samantha Forde when papers are accepted.

• Data
  • phage metagenomes from CAMERA: Once you login CAMERA portal, click “Data Query” tab under “Browse Data”, there is a table with all projects; then go to the second page, you will see “CAM_PROJ_BroadPhageGenomes” and “CAM_PROJ_BroadPhage” projects. If you click the accession number, all details are there.
  • Guillaume will check what is there
  • Tom: check filter size, may remove a lot of the bacteria and archaea

• Scheduling in person meeting
  • No date through mid-April that all can make
  • Samantha Forde wants to meet in May or early June - combine?
  • Guillaume may come to SF in late Feb to work on SFams updating

• Tim Laurant started Monday as Bioinformatics person at Gladstone

• Problems with compute cluster in Davis
  • Maybe move SFams updates to QB3 cluster
  • A UCSF person (with ID number) would need to be in charge

• SFams updates
  • Guillaume: updating code almost ready to go
  • Tom will review to see if it works on QB3
  • Stephen: should include check for start and stop codons
  • Won't switch to LAST for now
  • Many new genomes - need to release soon

• Future of SFams
  • Add single cell amplified genomes, assembled metagenomes
    • With quality control for bad assemblies
    • Represent poorly sampled lineages
    • Focus on marine maybe if too many total
  • JE: worthwhile if not too burdensome
  • Who else is doing this? Sanger?
    • Who has a connection to start that conversation
  • Stephen has a lot of ideas about improvements
  • Focus on short read classification problems
    • Might be short sighted to optimize for short reads since reads are getting longer
  • Most current users are employing SFams for annotating genomes (from diverse lineages)
  • Issues are more general than SFams
  • JE: Main concern is spending a lot of time/resources on maintenance and updates, but the research is important

• Josh talked to Jack Gilbert
  • Beta-diversity niche modeling
    • Applications: map of community classifications, predicting novel communities
  • Forensic project with Naval Research Lab
  • Data
    • Earth microbiome project (16S)
    • No global shotgun metagenomics data set
    • Gilbert uses PRMT tool to map from 16S to functions
  • Other overlaps for collaboration
    • Functional diversity mapping (paper in press on CO2 flux in English Channel)
    • We should act on this soon to carve our our part

• Southern Oceans data set (positive selection analyses questioned)
  • Might be problematic even to use the data