1 / 18

Invited Talk Honoring David Kingsbury Gordon and Betty Moore Foundation Palo Alto, CA

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

umika
Download Presentation

Invited Talk Honoring David Kingsbury Gordon and Betty Moore Foundation Palo Alto, CA

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation 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 TogetherTwo 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 Source: Phil Papadopoulos, SDSC, Calit2 ~200TB Sun X4500 Storage 10GbE 512 Processors ~5 Teraflops ~ 200 Terabytes Storage 1GbE and 10GbE Switched/ Routed Core

  6. CAMERA Timeline Start of CAMERA Availability of GOS Data (0.7) CAMERA 1.2.6 CAMERA 1.3.2.28 CAMERA 1.0 CAMERA 2.0 2006 2007 2008 2009 Alpha Preview of CAMERA 2.0 CAMERA 2.0 Beta Source: Jeff Grethe, NCMIR, CAMERA, UCSD

  7. Marine Genome Sequencing Project – CAMERA Anchor Dataset Launched March 13, 2007 Each Sample ~2000 Microbial Species Specify Ocean Data Measuring the Genetic Diversity of Ocean Microbes

  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 ExpandingEnvironmental Metagenomics Datasets March 16, 2008 Rapidly Expanding to Include New Community Datasets Now Releasing An Additional Dataset Per Week!

  10. CAMERA Timeline Start of CAMERA Availability of GOS Data (0.7) CAMERA 1.2.6 CAMERA 1.3.2.28 CAMERA 1.0 CAMERA 2.0 2006 2007 2008 2009 Alpha Preview of CAMERA 2.0 CAMERA 2.0 Beta Source: Jeff Grethe, NCMIR, CAMERA, UCSD

  11. Current CAMERA InterfaceMarch 17, 2009

  12. The CAMERA Project Has Established a GlobalMarine 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 Photo Credit: Alan Decker Feb. 29, 2008 Ginger Armbrust’s Diatoms: Micrographs, Chromosomes, Genetic Assembly 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 Start of CAMERA Availability of GOS Data (0.7) CAMERA 1.2.6 CAMERA 1.3.2.28 CAMERA 1.0 CAMERA 2.0 2006 2007 2008 2009 Alpha Preview of CAMERA 2.0 CAMERA 2.0 Beta 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 Source: Paul Gilna, John Wooley, Calit2 • 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

  18. GBMF Data Acquisition Pipeline:A New Data Submission Paradigm-Metadata First! Source: Paul Gilna, Calit2 Solexa and SOLiD Next! CAMERA sends acknowledgement to Investigator, Seq. Group, GBMF Seq. Group Upload data to CAMERA (& Investigator) Investigator submits proposal to GBMF Investigator submits metadata to CAMERA Data & Metadata Released in six months Metadata now collected before sequence data: GSC-compliant Project-ID serves as acceptance-proof Sample is Received and Sequenced Seq. Group send barcoded sample “kit” to investigators Webb Miller and Stephan C. Schuster, and Roche / 454 Genome Sequencer

More Related