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
- 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, firstname.lastname@example.org
- John Wooley, Co-PI, email@example.com
- Paul Gilna, Executive Director of CAMERA, firstname.lastname@example.org
- Greg Hidley, email@example.com. Display Wall and Other IT Guru.
- Kayo Arima, firstname.lastname@example.org. Outreach.
- Weizhong Li, email@example.com. Mathematician/Data analysis.
- Sriram Krishnan, firstname.lastname@example.org. CAMERA labs.
- Mason Katz, email@example.com. Software/hardware. Supervises Adam and Brian.
- Brian Fox, firstname.lastname@example.org. New data sets. Brian imports data from PIs
- Adam Brust, email@example.com. IT support.
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?