[CAnet - news] Cyberinfrastructure & Optical Networks for Microbial Ecology Research

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[Some excerpts from UCSD press release-- BSA]

http://ucsdnews.ucsd.edu/newsrel/general/CAMERA.asp
            
	

January 17, 2006

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."
The CAMERA project builds on pioneering efforts in metagenomics to sequence
the genomes of entire microbial communities, often comprising thousands of
species. 

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.

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.


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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