Building an OptIPlanet collaboratory to support microbial metagenomics

Future Generation Computer Systems

Volumn 25, Issue 2, 2009, Pages 124-131

  Smarr, Larry ^a   Gilna, Paul ^a   Papadopoulos, Phil ^a,b   DeFanti, Thomas A ^a   Hidley, Greg ^a   Wooley, John ^a   Virginia Armbrust, E ^c   Rohwer, Forest ^d   Frost, Eric ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

CAMERA; Metagenomics; Microbial; OptIPortal; OptIPuter

Indexed keywords

BASE PAIRS; CAMERA; COLLABORATORY; DATA-INTENSIVE; GLOBAL VIEWS; LOCAL ENVIRONMENTS; METAGENOMICS; MICROBIAL; MICROBIAL GENOMES; OPTIPORTAL; OPTIPUTER; REMOTE USERS; SCIENCE APPLICATIONS; SCIENTIFIC DATA;

EID: 52949120285     PISSN: 0167739X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.future.2008.06.009     Document Type: Article

References (37)

1. For a comprehensive recent review see. The New Science of Metagenomics-Revealing the Secrets of Our Microbial Planet (2007), National Research Council, National Academy Press
2. See www.optIPuter.net for a list of participants and publications. The authors acknowledge the National Science Foundation in providing funding for the OptIPuter project under the auspices of grant # OCI-0225642
3. The Gordon and Betty Moore Foundation (www.moore.org), established in September 2000, works in collaboration with grantees and other partners to achieve significant and measurable outcomes in three areas: environmental conservation, science, and the San Francisco Bay Area. In April 2004, the foundation launched its 10-year Marine Microbiology Initiative with the goal of attaining new knowledge regarding the composition, function, and ecological role of microbial communities in the world's oceans. The authors acknowledge the Gordon & Betty Moore Foundation in providing funding for the CAMERA project under the auspices of grant #951.
4. The California Institute for Telecommunications and Information Technology (www.calit2.net), a partnership between UC San Diego and UC Irvine, houses more than 1000 researchers organized around more than 50 projects on the future of telecommunications and information technology and how these technologies will transform a range of applications important to the economy and citizens' quality of life.
5. J. Craig Venter Institute (www.venterinstitute.org) is a not-for-profit research institute dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., Venter Institute is home to approximately 200 staff and scientists with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. J. Craig Venter Institute is a 501(c)(3) organization.
6. The Center for Earth Observations and Applications (http://ceoa.ucsd.edu) was established in November 2005 by UCSD to stimulate support and coordinate sustained research and applications in Earth observations. Led by Scripps Institution of Oceanography in partnership with Calit2 and other campus organizations, CEOA provides an integrating vision for work across the spectrum of natural, physical, and social sciences, engineering, and information technology related to Earth observations and applications. Working through CEOA is Terry Gasterland's Scripps Genome Center (see http://ucsdnews.ucsd.edu/newsrel/science/GaasterlandGenomeCenter.asp), which is producing annotations of the microbial metagenomics data.
7. In 2005, the San Diego Supercomputer Center (SDSC; www.sdsc.edu) celebrated two decades of enabling international science and engineering discoveries through advances in computational science and high-performance computing. Continuing this legacy into the era of cyberinfrastructure, SDSC is a strategic resource to academia and industry, providing leadership in data cyberinfrastructure, particularly with respect to data curation, management, and preservation, data-oriented high-performance computing, and cyberinfrastructure-enabled science and engineering. SDSC is an organized research unit of the University of California, San Diego, and one of the founding sites of NSF's TeraGrid.
8. For a history of Woese's microbial revolution, see. Science 276 May (1997) 699-702. http://www.sciencemag.org/cgi/content/full/276/5313/699 www.sciencemag.org/cgi/content/full/276/5313/699, ai.arc.nasa.gov/news_stories/news_detail.cfm?ID=274, or http://en.wikipedia.org/wiki/Carl_Woese
9. 16S rRNA is found in the small ribosomal subunit of microbial ribosomes and the mitochondria and chloroplasts ribosomes of eukaryotes. Since ribosomes are essential for DNA transcription to form proteins, most ribosomal RNA mutations are deleterious, resulting in a very slow evolution of 16S rRNA. This makes it a very good molecule to use to compare organisms that may have diverged as far back as 3 or 4 billion years ago. For more on 16S rRNA sequencing, see www.microbeworld.org/htm/aboutmicro/tools/genetic.htm.
10. A nice diagram of the tree is at http://genome.jgi-psf.org/tre_home.html or http://en.wikipedia.org/wiki/Image:PhylogeneticTree.jpg. For more on the biology of creatures in the Tree of Life, See http://tolweb.org/tree.
11. For the story of the whole of life's evolution, see. Fortey R. Life: A Natural History of the First Four Billion Years of Life on Earth (1998), Alfred A. Knopf, NY
12. For a very readable account of the Cambrian explosion of multi-cellular body plans, see. Gould S.J. Wonderful Life: The Burgess Shale and the Nature of History (1989), W.W. Norton and Co.
13. Pace N. The large-scale structure of the tree of life. In: Sapp J. (Ed). Microbial Phylogeny and Evolution: Concepts and Controversies (2005), Oxford Univ. Press
14. Craig Venter J., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 April (2004) 66
15. Falkowski P., and de Vargas C. Shotgun sequencing in the sea: A blast from the past?. Science 304 April (2004) 58. http://www.genomenewsnetwork.org/articles/2004/03/04/sargasso.php (and commentary) See also news story linking to Sorcerer II expedition at www.genomenewsnetwork.org/articles/2004/03/04/sargasso.php
16. See for more details http://en.wikipedia.org/wiki/Shotgun_sequencing
17. See www.ncbi.nih.gov. As of August 2008, GenBank held more than 100 billion bases from more than 165,000 species.
18. See, www.sorcerer2expedition.org
19. For a recent review, see Kevin Chen, Lior Pachter, Bioinformatics for whole-genome shotgun sequencing of microbial communities, PLoS Computational Biology: http://compbiol.plosjournals.org/perlserv/?request=get-document%26doi=10.1371/journal.pcbi.0010024 or
20. Tringe S.G., von Mering C., Kobayashi A., Salamov A.A., Chen K., Chang H.W., Podar M., Short J.M., Mathur E.J., Detter J.C., Bork P., Hugenholtz P., and Rubin E.M. Comparative Metagenomics of Microbial Communities. Science 308 April (2005) 554
21. Science 307 March (2005) 1558
22. See, www.syntheticgenomics.com
23. Look S., et al. PNAS 83 (1986) 6283
24. http://news-service.stanford.edu/news/2006/may24/criddle-052406.html
25. See, www.whoi.edu/mr/pr.do?id=919
26. www.nlr.net
27. www.glif.is
28. The usable server room was doubled to 2000sf, we added a 500kva transformer and doubled to twelve the 225A breakers, added a StarLine modular power grid power distribution system, and added 66 tons of cooling, ducts and registers.
29. Rocks Core Development is sponsored by the NSF as part of award #OCI-438741. www.rocksclusters.org
30. See, for instance, The OptIPuter, Quartzite, and Starlight Projects: A Campus to Global-Scale Testbed for Optical Technologies Enabling LambdaGrid Computing: http://www.optiputer.net/publications/articles/Smarr-OFC-2005.pdf.
31. www.teragrid.org
32. See accompanying FGCS article on OptIPortals
33. The tiled wall uses 3×5 16 Dell UltraSharp 2407FP Wide Flat Panels, each with a native resolution of 1920×1200 pixels. The Linux cluster supporting the OptIPortals has 8 Dell Dimension 9200 with Dual Intel E6700 2.66 GHz processors and Dual EVGA GeForce 7950 GX2 GPUs, together with 4GB RAM with a 160GB Hard Drive per PC.
34. The Moderate Resolution Imaging Spectro-radiometer (MODIS) instrument is on the NASA Aqua Earth-observing satellite. Goddard Space Flight Center hosts the MODIS Data Processing System (https://modaps.nascom.nasa.gov:8499).
35. These network connections serve 3 clusters: (1) 32-node compute cluster. Each compute node is dual-socket quad-core Xeon E5345 2.33 GHz with 16 GB RAM, the whole system is 256 cores. Interconnect is GigE and infiniband. (2) 4-node cluster for testing code and administrative changes before they get put on the 32-node cluster. Each compute node is a dual-socket dual-core AMD 2218 2.66 GHz, 4 GB RAM. (3) Visualization cluster. 8 viz nodes are dual-socket dual-core AMD 2216 2.4 GHz, 8 GB RAM, Nvidia 8800GTX card. Interconnect is GigE. There are fifteen 30" monitors in the 5 row 3 column display wall.
36. See accompanying FGCS article on StarCAVE and Varrier.
37. The Joint Center for Structural Genomics (GM062411-05) is funded by the National Institute for General Medical Sciences, as part of the Protein Structure Initiative of the National Institutes of Health. It is a multi-institutional consortium with major activities at the Scripps Research Institution; the Genomics Institute of the Novartis Research Foundation; the University of California, San Diego; and the Stanford Synchrotron Radiation Laboratory at Stanford University. See www.jcsg.org.