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Creating a Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (a.k.a. CAMERA)

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09.03.18 …

09.03.18
Invited Talk
Honoring David Kingsbury
Gordon and Betty Moore Foundation
Title: Creating a Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (a.k.a. CAMERA)
Palo Alto, CA

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  • This is a production cluster with it’s own Force10 e1200 switch. It is connected to quartzite and is labeled as the “CAMERA Force10 E1200”. We built CAMERA this way because of technology deployed successfully in Quartzite
  • NIEeS = The National Institute for Environmental eScience (NIEeS) a collaboration between the National Environment Research Council and the University of Cambridge

Transcript

  • 1. Creating a Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (a.k.a. CAMERA) Invited Talk Honoring David Kingsbury Gordon and Betty Moore Foundation Palo Alto, CA March 18, 2009 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technology Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD
  • 2. The Beards are Still Working Together Two Decades Later! David Kingsbury and John Wooley NSF 1987 Larry Smarr NCSA 1985
  • 3. PI Larry Smarr David Kingsbury Call to LS July 31, 2005 Grant Announced January 17, 2006
  • 4. The Moore Foundation Was an Early Funder As The National Consensus Emerged “ The emerging field of metagenomics, where the DNA of entire communities of microbes is studied simultaneously, presents the greatest opportunity -- perhaps since the invention of the microscope – to revolutionize understanding of the microbial world.” – National Research Council March 27, 2007 NRC Report: Metagenomic data should be made publicly available in international archives as rapidly as possible.
  • 5. Calit2 Microbial Metagenomics Cluster- Next Generation Optically Linked Science Data Server 512 Processors ~5 Teraflops ~ 200 Terabytes Storage 1GbE and 10GbE Switched/ Routed Core ~200TB Sun X4500 Storage 10GbE Source: Phil Papadopoulos, SDSC, Calit2
  • 6. CAMERA Timeline 2006 2007 2008 2009 Alpha Preview of CAMERA 2.0 CAMERA 1.3.2.28 CAMERA 2.0 CAMERA 2.0 Beta Start of CAMERA Availability of GOS Data (0.7) CAMERA 1.0 CAMERA 1.2.6 Source: Jeff Grethe, NCMIR, CAMERA, UCSD
  • 7. Marine Genome Sequencing Project – CAMERA Anchor Dataset Launched March 13, 2007 Measuring the Genetic Diversity of Ocean Microbes Specify Ocean Data Each Sample ~2000 Microbial Species
  • 8. Moore Foundation Enabled the Sequencing of the Full Genome Sequence of 155+ Marine Microbes www.moore.org/microgenome
  • 9. CAMERA Houses the Community’s Expanding Environmental Metagenomics Datasets Rapidly Expanding to Include New Community Datasets Now Releasing An Additional Dataset Per Week! March 16, 2008
  • 10. CAMERA Timeline 2006 2007 2008 2009 Alpha Preview of CAMERA 2.0 CAMERA 1.3.2.28 CAMERA 2.0 CAMERA 2.0 Beta Start of CAMERA Availability of GOS Data (0.7) CAMERA 1.0 CAMERA 1.2.6 Source: Jeff Grethe, NCMIR, CAMERA, UCSD
  • 11. Current CAMERA Interface March 17, 2009
  • 12. The CAMERA Project Has Established a Global Marine Microbial Metagenomics Cyber-Community 2700 Registered Users From 76 Countries
  • 13. Building the Metagenomics Community Through Annual Meetings
  • 14. Prototyping Next Generation User Access and Analysis- Between Calit2 and U Washington Ginger Armbrust’s Diatoms: Micrographs, Chromosomes, Genetic Assembly Photo Credit: Alan Decker Feb. 29, 2008 iHDTV: 1500 Mbits/sec Calit2 to UW Research Channel Over NLR
    • The Disease is Spreading!
    • c.f. Dave Karl, Hawaii
    • Ed DeLong, MIT
  • 15. CAMERA Timeline 2006 2007 2008 2009 Alpha Preview of CAMERA 2.0 CAMERA 1.3.2.28 CAMERA 2.0 CAMERA 2.0 Beta Start of CAMERA Availability of GOS Data (0.7) CAMERA 1.0 CAMERA 1.2.6 Source: Jeff Grethe, NCMIR, CAMERA, UCSD
  • 16. Calit2 is Creating CAMERA 2.0 -- Advanced Cyberinfrastructure Service Oriented Architecture Source: CAMERA CTO Mark Ellisman
  • 17. CAMERA Is a Contributing Member of the Genome Standards Consortium
    • Standardizing Contextual Metadata
      • Members from EU, UK, US
    • Goals are to Promote
      • Standardization of Genomic Descriptions
      • Exchange & Integration of Genomic Data
    • Metadata Standardization Key Enabler
      • MIMS: Min Info for Metagenomic Sample
      • GCDML: Standard format
    • NSF Research Coordination Network for Genomic Standards Consortium (John Wooley = PI)
      • Allows Calit2 to Support Genomic and Metagenomic Standards
      • Extends the GSC to Broader Biocommunity
      • Provides Through CAMERA Another Channel for GBMF Investigators and CAMERA to be Central to Community Dialogue
    Source: Paul Gilna, John Wooley, Calit2
  • 18. GBMF Data Acquisition Pipeline: A New Data Submission Paradigm-Metadata First! Metadata now collected before sequence data: GSC-compliant Project-ID serves as acceptance-proof Sample is Received and Sequenced Solexa and SOLiD Next! Webb Miller and Stephan C. Schuster, and Roche / 454 Genome Sequencer Source: Paul Gilna, Calit2 Investigator submits proposal to GBMF Investigator submits metadata to CAMERA CAMERA sends acknowledgement to Investigator, Seq. Group, GBMF Seq. Group send barcoded sample “kit” to investigators Seq. Group Upload data to CAMERA (& Investigator) Data & Metadata Released in six months