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?