Biotech News - UC San Diego Partners with Venter Institute to Build

UC San Diego Partners with Venter Institute to Build
Community Cyberinfrastructure for Advanced Marine
Microbial Ecology Research and Analysis
Gordon and Betty Moore Foundation Awards

$24.5 Million Grant to Advance Metagenomics Research

By Doug Ramsey

Larry Smarr, Director, Calit2 and Principal Investigator, CAMERA
Researchers at UCSD will build a state-of-the-art computational
resource and develop software tools to decipher the genetic code of
communities of microbial life in the world's oceans. The new
resource will help scientists understand how microbes function in
their natural ecosystems, enable studies on the effect humans are
having on the environment, as well as permit insight into the
evolution of life on Earth. The UCSD Division of the California
Institute for Telecommunications and Information Technology (Calit2)
will lead the project in partnership with J. Craig Venter Institute
(Venter Institute) in Rockville, MD, and UCSD's Center for Earth
Observations and Applications (CEOA) at Scripps Institution of
Oceanography.

"This prototype cyberinfrastructure will be used by scientists
studying marine life and ecosystems to examine—in an unprecedented
manner—the genomic complexities of natural communities of micro-
organisms as they have evolved in their local environments," said
UCSD Chancellor Marye Anne Fox. "This project will change the way
large-scale science can be conducted and we are proud to develop
this world-class and pioneering facility on our UCSD campus."

Sorcerer II circumnavigation route

The Gordon and Betty Moore Foundation has awarded $24.5 million over
seven years to create the Community Cyberinfrastructure for Advanced
Marine Microbial Ecology Research and Analysis (CAMERA). Scientists
will use CAMERA for metagenomics research—analyzing microbial
genomic sequence data in the context of other microbial species, as
well as in comparison to a variety of other "metadata" such as the
chemical and physical conditions in which microbes are sampled.

Craig Venter (left) sampling in Sargasso Sea with Tony Knapp,
director of Bermuda Biological Station for Research
"The explosion of data from the collection and sequencing of marine
microbes requires a completely novel approach to storing, accessing,
mining, analyzing, and drawing conclusions from this rich new wealth
of information," said co-investigator J. Craig Venter, Ph.D.,
president of Venter Institute. "The goal is to create a community
resource to house all metagenomic data that will facilitate and
advance knowledge of marine microbial ecology, other natural
environments, and evolutionary biology."

The CAMERA project builds on pioneering efforts in metagenomics to
sequence the genomes of entire microbial communities, often
comprising thousands of species. The largest such effort is Venter
Institute's Sorcerer II Expedition, for which sequencing is funded
by the Moore Foundation. The Expedition is developing the first
large-scale genomic survey of microbial life in the world's oceans
to produce the largest gene catalogue ever assembled. Sorcerer II is
expected to more than double the number of protein sequences
currently available in the National Institutes of Health's GenBank.
The metagenomics database will include new sequences, genes and gene
families, together with their annotations and associated
environmental metadata.

Slide with bacteria from Venter Institute's Sorcerer II Expedition
The move from traditional organism genome databases to the CAMERA-
based environmental metagenomics data storage and computational
complex requires development of a more complex cyber-architecture.
Using dedicated optical circuits, CAMERA will permit scientists to
connect their local laboratory PC clusters directly to the CAMERA
database and tools using the National LambdaRail or international
optical circuits, resulting in up to a hundred-fold increase in
bandwidth over current standards.

The enhanced connectivity is based on a model pioneered by the
OptIPuter project and funded by the National Science
Foundation. "Linking Venter Institute to Calit2 will be the first
persistent application of the OptIPuter high-
performance `collaboratory'," said Calit2 director Larry Smarr,
Ph.D., principal investigator on both the OptIPuter and CAMERA
projects. "The architecture is quite general and will be quickly
adaptable to other areas of data-intensive science." Collaboratories
are virtual laboratories where scientists can collaborate on
research from dispersed locations—interacting with colleagues,
accessing instrumentation, sharing data and computational resources,
and accessing information from remote digital libraries.

Calit2 will also partner with UCSD's San Diego Supercomputer Center
(SDSC) to create a next-generation science data server complex,
which couples the Calit2 and SDSC middleware, compute, and storage
capabilities with the NSF's TeraGrid distributed, high- performance
computing facility in a unified Service Oriented Architecture.
SDSC's Philip Papadopoulos noted that, "the CAMERA complex will have
a thousand processors of dedicated local cluster computing and
several hundred terabytes of replicated data storage, backed up by
the SDSC and TeraGrid high performance compute and storage
complexes." This will enable "scalable computing" resources to be
applied to a wide range of computational tools to tackle the
computationally intense questions derived from the larger
metagenomic data collection.

Calit2 and Venter Institute will also support a series of training
sessions and specialized seminars on this emerging discipline, as
well as provide space for environmental metagenomics visitors to
collaborate with CAMERA specialists. Over the next few years, CAMERA
is expected to include other environmental or medical metagenomic
datasets, as the novel cyberinfrastructure enables research in other
disciplines.

The Moore Foundation grant, in part, contributes to the $1 billion
fundraising goal of The Campaign for UCSD: Imagine What's Next.

Media Contacts:

Doug Ramsey, Calit2, (858) 822-5825
Melanie Wranaker, Venter Institute, (301) 943-8879
Mario Aguilera or Cindy Clark, Scripps/CEOA, (858) 534-3624
Ashley Wood, SDSC, (858) 534-8363
Alex Barnum, Moore Foundation, (415) 561-7414
Debra Kain, UCSD Health Sciences, (619) 543-6163

Background

The goal of the CAMERA project is to create important advances in
the knowledge of evolutionary biology and microbial ecology in
marine and other natural environments.

"Metagenomics has the potential to revolutionize our understanding
of microbial ecology in a large number of environments," said David
Kingsbury, Ph.D., chief program officer for science at the Moore
Foundation. "The major factor limiting its further progress has been
the management of the very large quantities of data. We are
delighted to be able to support the development of this community
resource at one of the world's premier sites for high-speed
networking and high-performance scientific computing."

In addition to Sorcerer II's ecological genomic data, the CAMERA
database will be augmented by the soon-to-be-completed genomes of
more than 150 critical marine microbes, also funded by the Moore
Foundation, for comparative genomics studies. Venter Institute's
Marv Frazier, Ph.D., co-principal investigator with Larry Smarr,
said "We are looking forward to providing a metagenomics server
complex for the data produced by our colleagues at the Department of
Energy's Joint Genome Institute."

Scripps researchers will contribute expertise in modeling, analysis
and information management across Earth-science observing
systems. "We also have a set of world-class researchers in microbial
ecology and annotating marine genomic data," said Scripps Deputy
Director John Orcutt, who directs the CEOA and is a co-investigator
on the new project along with Terry Gaasterland, director of the
Scripps Genome Center launched last October. Experts at Venter
Institute and the Scripps Genome Center will create annotations for
much of the CAMERA genomic data.

The project brings together new technologies of high-throughput DNA
sequencing and metagenomic analysis tools on the one hand, and
cyberinfrastructure innovations on the other. Together, they will
provide new tools to help marine microbial ecologists access and
derive inferences from the massive data sets. The tools will allow
ecologists, for example, to analyze families of proteins and conduct
comparative analyses across multiple genomes.

"Each individual sequence is no longer just a piece of a genome. It
is part of an entire biological community," said Peter Arzberger,
Ph.D., director of the NIH-funded National Biomedical Computation
Resources (NBCR), and lead author of the CAMERA grant
proposal. "CAMERA will build on the NBCR software tools and user
portal to explore the metagenomics data."

NBCR has links to the UCSD School of Medicine, and co-investigator
John Wooley is affiliated with the Skaggs School of Pharmacy and
Pharmaceutical Sciences. "Along with providing a novel approach to
advancing fundamental biological knowledge, analysis of the marine
genome data will allow us insight into natural marine products and
how they can be applied for pharmacy and medicine," said Wooley, the
university's Associate Vice Chancellor for Research. "The new
resource will greatly enhance our health science researchers'
ability to advance the development of new drugs and therapies from
the ocean's resources to combat cancer and neurodegenerative and
other diseases."

Venter Institute will make available a large collection of community-
developed genome analysis software tools. The CAMERA tools will
address the needs of two groups of users. The first group comprises
potential users with little programming ability using web-based
tools to explore data and visualization tools to interpret the
results. The second group comprises bioinformatics experts with
their own tools and programming. CAMERA will encourage this later
group to contribute their software analysis tools, thus engaging the
broader community in strengthening this international resource.

Other co-investigators on the CAMERA project include Venter
Institute's Saul Kravitz, Aaron Halpern and Jonathan Eisen, as well
as UCSD-based scientists Tom DeFanti and Ingolf Krueger.

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