Launching the Global Community Cyberinfrastructure for Advanced Marine Microbial Research and Analysis (CAMERA)
UC San Diego Makes Venter Institute's Global Ocean Sampling (GOS) Expedition Microbial Metagenomic Data and Computational Tools Available to Scientists Worldwide
Scientists and engineers at the University of California, San Diego and the J. Craig Venter Institute (JCVI) have flipped the virtual switch on the first cyberinfrastructure customized to serve the marine microbial metagenomics community. At the heart of the cyberinfrastructure is a new, high-performance computer and storage complex funded by the Gordon and Betty Moore Foundation and located in UC San Diego's Atkinson Hall, headquarters of the California Institute for Telecommunications and Information Technology (Calit2), a partnership of UC San Diego and UC Irvine.
The computer complex enables analysis of a vast array of biocomplexity data housed in the Community Cyberinfrastructure for Advanced Marine Microbial Research and Analysis (CAMERA). It includes environmental metagenomic and genomic sequence data, associated environmental parameters ("metadata"), precomputed search results, and cross-analysis of environmental samples. While end users can manipulate the data over the web or over dedicated optical circuits, CAMERA permits scientists to connect their local laboratory computers directly to the CAMERA database and tools using the National LambdaRail, Internet2's NewNet, or international optical circuits, resulting in up to a hundred-fold increase in bandwidth over the conventional shared Internet.
CAMERA has been in beta testing since January and today launched the first production version of its database and computational resources. Simultaneously, at a news conference held in Washington D.C., researchers announced the first scientific findings based on sequences and metadata deposited in CAMERA by JCVI's Global Ocean Sampling (GOS) Expedition. The findings are published as articles in the Oceanic Metagenomics collection in the March 2007 issue of PLoS Biology, including "CAMERA: A Community Resource for Metagenomics," a four-page introduction to the project by JCVI's Rekha Seshadri, Saul Kravitz and Marvin Frazier, with Calit2's Larry Smarr and Paul Gilna [PLoS Biology, March 2007 | Volume 5 | Issue 3 | e75].
"A new cyberinfrastructure architecture is required to support the field of genomics as it transitions to the study of metagenomics," said CAMERA principal investigator Larry Smarr, a professor of computer science and engineering at UC San Diego and director of Calit2. "The infrastructure will create a virtual domain for global data and knowledge sharing by this emerging research community."
The Gordon and Betty Moore Foundation funded the CAMERA project in January 2006 with $24.5 million over seven years, building on its previous support for Venter's ambitious program to sequence marine microbes. "We asked Calit2 to join with us on this project because Larry Smarr and his National Science Foundation-funded OptIPuter team were already pioneering and prototyping infrastructure for large-scale, distributed scientific collaboration," said JCVI founder and chairman, Craig Venter. "CAMERA's database and computational tools are truly global resources, and they will be accelerating and broadening what the community learns from the GOS Expedition and future metagenomic research efforts."
"We are proud that UC San Diego can bring together the strengths of our world-renowned research units to create CAMERA's state-of-the-art cyberinfrastructure to support this important new scientific discipline," said the university's Chancellor, Marye Anne Fox. CAMERA is being developed by Calit2 at UC San Diego in collaboration with the JCVI, the university's Center for Earth Observations and Applications (anchored by the Scripps Institution of Oceanography), the San Diego Supercomputer Center, and the University of California, Davis.
The CAMERA database is different from most other genomic repositories because it was designed to accommodate environmental metadata as well as the sequence data derived from DNA samples. Even before the production version went online, a beta release of the database had been accessed by over 240 research scientists and students at more than 40 U.S. institutions, as well as users in at least ten foreign countries. Access to the CAMERA resources is free; users who register agree to abide by the terms of the Convention on Biological Diversity, in recognition of the many international sources of the data housed in CAMERA.
The sequence data from the GOS study have also been deposited in the National Institutes of Health-funded public database GenBank, however CAMERA is designed with metagenomic researchers in mind. "If a scientist queries our database for a particular set of sequence data, he or she would also get back all the metadata associated with each metagenomic sequence read," said Paul Gilna, executive director of CAMERA. "This is a very useful feature because the metadata could provide clues to understanding differences between microbial specimens, especially if you are comparing microbes that live in very different ocean environments. Our metadata, more generally, will serve to advance marine environmental biology and ecology research."
CAMERA builds on the NSF funded OptIPuter research project, which is prototyping a global-scale end-to-end cyberinfrastructure backplane, stretching from a high-resolution visualization cluster in the researcher's lab, over dedicated one- or ten-gigabit per second lightpaths on optical fiber, to remote data and compute servers that may be located next door or thousands of miles away. Over the next few years, the dedicated but reconfigurable optical connectivity will provide metagenomics researchers with the freedom to work with data objects that are orders-of-magnitude larger than those transmitted over the conventional shared Internet.
The tiled LCD visualization displays, known as OptIPortals, scale from tens of millions to hundreds of million pixels. They provide the end user with the "pixel real estate" needed to explore the complexities of metagenomic data. Developed by the Electronic Visualization Laboratory at the University of Illinois at Chicago and Calit2, they are already installed at the JCVI and UC San Diego, and more are now being installed in partner metagenomics labs at the University of Washington, San Diego State University, MIT and elsewhere, including several international labs.
The CAMERA data resides on servers located at Calit2's headquarters on the UC San Diego campus, including a large production server consisting of a 512-CPU cluster (approximately 5 trillion floating-point operations per second, or "teraflops") with roughly 200 trillion bytes ("terabytes") of dedicated storage, all built on the SDSC Rocks (http://www.rocksclusters.org) cluster configuration software. A separate server at Calit2 hosts tools for analyses, tools for transferring large data sets and applications, and also a web-based interface for the user community.
Data and Tools
In addition to data from the GOS Expedition, the CAMERA database includes metagenomic data from the Marine virome data collection from Forest Rohwer's group at San Diego State University, and the metagenomic data from the Hawaii Ocean Time Series Station ALOHA contributed by Ed DeLong's group at MIT. Today's release will also allow users to access or search 68 completed genomes from the 155 genomes included in the Moore Microbial Sequencing project being conducted at the JCVI. Large reference collections of relevant sequence data are available for search, including non-identical amino acids, microbial, viral, and fungal sequence and peptides, as well as sequences and peptides from microbial eukaryotes.
"Since CAMERA is designed to be a community-driven resource, we will routinely introduce additional data sets based on input and priorities set by the metagenomics community," said Marv Fazier, VP for Research at JCVI and co-principal investigator on the CAMERA project. "Our plan is that in year two, the additional data will include further phases of GOS, additional members of the Moore 155 genome sets as they become available, the Department of Energy's Joint Genome Institute [JGI] metagenomic data sets, as well as the data from projects deposited at the National Institutes of Health's National Center for Biotechnology Information [NCBI]."
Researchers working on pre-release versions of the GOS data used initial analysis tools developed at the JCVI, including a number of variants of BLAST nucleotide and amino acid sequence search tools that were allied to a metadata export capability. Tools in the pipeline will allow users to upload metagenomic data and their metadata, do metagenomic and whole microbial genome annotation, and conduct phylogenetic analyses.
Building the User Community
Through its new user software portal, the CAMERA website allows the user community to learn about the project and access applications and data sets. Meanwhile, leaders of the project have attracted a global set of metagenomics researchers by organizing an annual international metagenomics conference series at Calit2 (http://www.calit2.net/metagenomics2007/). CAMERA has also attracted leaders from the community to form an external Scientific Advisory Board.
With today's initial release of CAMERA capabilities, says principal investigator Smarr, "we have arrived at the beginning. The CAMERA team has built the foundation for an innovative and powerful cyberinfrastructure supporting biological research globally, with plans to enhance its capabilities and build the scientific community it serves. This infrastructure will now serve as a template or model for other large scientific communities requiring such an extensive level of computing, networking, data sharing, and collaboration."
Users interested in exploring and using the CAMERA resource should go to http://www.calit2.net/newsroom/article.php?id=1069 and follow the instructions for registration. Registration is free and open to all interested in using CAMERA in their research.
The California Institute for Telecommunications and Information Technology, a partnership between UC San Diego and UC Irvine, houses over 1,000 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 California economy and its citizens' quality of life. http://www.calit2.net
About J. Craig Venter Institute
The J. Craig Venter Institute is a not-for-profit research institute which through its two operating divisions, The Institute for Genomic Research (TIGR) and The Center for the Advancement of Genomics (TCAG) advances 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., the JCVI is home to approximately 500 scientists and staff 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. The JCVI is a 501 (c)(3) organization.
About Moore Foundation
The Gordon and Betty Moore Foundation, 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. http://www.moore.org
The Center for Earth Observations and Applications (CEOA) was established in November 2005 by UC San Diego to stimulate support and coordinate sustained research and applications in Earth observations at the university. Led by UC San Diego's 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. http://ceoa.ucsd.edu
The San Diego Supercomputer Center (SDSC) enables 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. http://www.sdsc.edu
About UC San Diego
Since its founding just four and a half decades ago, UC San Diego — one of the ten campuses in the world-renowned University of California system — has rapidly achieved the status as one of the top institutions in the nation for higher education and research. With annual research funding of more than $650 million, UC San Diego ranks fifth in the nation and first in the UC system in federal R&D expenditures. UC San Diego faculty and graduate programs have been ranked 10th best in the nation by the National Research Council. The campus, which enrolls more than 25,000 students, has one of the nation's highest percentages of faculty elected to the prestigious national academies.
The OptIPuter is a five-year, $13.5-million project funded by the National Science Foundation. It enables scientists who are generating massive amounts of data to interactively visualize, analyze, and correlate their data from multiple storage sites connected via optical networks. Calit2 [UC San Diego and UC Irvine] and the University of Illinois at Chicago (UIC) lead the research team, with academic partners at Northwestern University; San Diego State University; University of Southern California/Information Sciences Institute; University of Texas A&M; University of Illinois at Urbana-Champaign/National Center for Supercomputing Applications; and affiliate partners at the U.S. Geological Survey EROS Data Center, NASA Goddard, University of Amsterdam and SARA (Netherlands), KISTI (Korea), AIST (Japan), CRC (Canada), CICESE (Mexico); and, industrial partners Calient Networks, Cisco, Glimmerglass, HP, IBM, Lucent Technologies, Sun Microsystems and Telcordia. http://www.optiputer.net
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