Moore Notes CAMERA 4 18 08

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iSEEM team went to visit CAMERA on 4/18/08 This was our Quarterly Meeting as well as a chance to interact with CAMERA

Visitors were

  • Green Lab - Jessica Green, Liz Perry, James Dwyer
  • Pollard Lab - Katherine Pollard
  • Eisen Lab - Jonathan Eisen, Dongying Wu, Martin Wu

CAMERA personnel included

  • Larry Smarr, PI, lsmarr@ucsd.edu
  • John Wooley, Co-PI, jwooley@sdsc.edu
  • Paul Gilna, Executive Director of CAMERA, pgilna@soe.ucsd.edu
  • Greg Hidley, ghidley@soe.ucsd.edu. Display Wall and Other IT Guru.
  • Kayo Arima, weizhong@soe.ucsd.edu. Outreach.
  • Weizhong Li, weizhong@soe.ucsd.edu. Mathematician/Data analysis.
  • Sriram Krishnan, sriram@sdsc.edu. CAMERA labs.
  • Mason Katz, mjk@sdsc.edu. Software/hardware. Supervises Adam and Brian.
  • Brian Fox, bfox@soe.ucsd.edu. New data sets. Brian imports data from PIs
  • Adam Brust, abrust@soe.ucsd.edu. IT support.

Talks

Paul Gilna - What is CAMERA?

  • Mostly marine, microbiology/ecology focused, metagenomics data & tools
  • In year 3 of 5 year GBMF grant, partnership of CALIT2(75%) & JCVI (25%) (plus others)
  • Major resource = unassembled reads
  • Data: GOS (~8 million reads), GBFM researchers (~10 data sets), other community data
  • Processing: some assembly, translation
  • Metadata: time/date, geographic location, physical/chemical variables (standard format)
  • Compute cluster: 512 CPU
  • Interface: web portal, will have an API
  • Tools: mostly BLAST searches now, new tools to come

Jonathan Eisen - What are the Eisen lab CAMERA projects?

  • STAP: automated rRNA analysis
    • input = PCR or metagenomics rRNA sequences
    • output = taxonomy assignments, alignments (e.g. for OTU analysis)
  • Protein family analysis: classification for taxonomy, diversity, community characterization
    • input = translated metagenomics sequences (or ORFs)
    • output = HMM classifications of proteins

Jonathan Eisen, Katie Pollard, Jessica Green - What is iSEEM?

  • Summary of GBMF grant proposal
    • Microbial diversity (phylogenetics, abundance)
    • Molecular evolution & comparative genomics
    • Statistical metagenomics
  • Will focus initially on ~50 marker gene families, scored for phylogenetic informativeness

Mason Katz & others - How to integrate tools into CAMERA?

  • development sequence: (i) process, (ii) free-standing tool, (iii) pre-production, (iv) prodcution.
  • Opal: makes an API (web service) from an application

Questions from iSEEM PIs

  • How to get data from CAMERA? (Data link on website, web4.camera.calit2.net/files, or contact Weizhong)
  • Can we get compute accounts at CAMERA? (ask Mason)
  • Can we do db queries? (No)
  • How can we make suggestions regarding usability of CAMERA? (email camera-help, camera-info)
  • Who to contact about different kinds of questions?