http://www.sgi.com/newsroom/press_releases/2003/may/sars.html
Beijing Genomics Institute and Shanghai Institute of Materia
Medica Make Significant Progress on SARS Research Using SGI Origin
Family Servers
Mountain View, Calif. (May 20, 2003)--Separated by 676 miles,
two key research institutes at ground zero of the severe acute respiratory
syndrome (SARS) epidemic are conducting breakthrough research into
this mysterious disease, using SGI® servers to advance their
important work. The Beijing Genomics Institute (BGI) is identifying
the genomic basis for SARS in its many variations, while the Shanghai
Institute of Materia Medica (SIMM) is pursuing an effective pharmaceutical
vaccine or cure. Currently, there is no rapid test available to
confirm diagnosis of this newly characterized respiratory illness
in a timely manner, and there is no known effective treatment or
cure.
At SIMM, researchers are engaged in urgent SARS-related drug discovery
research that encompasses:
- Analyzing the genomic sequence of the virus thought to cause
SARS and identifying important proteins that may be involved in
the infection
- Predicting alterations in the identified proteins expected in
this mutable virus
- Constructing 3D models of these proteins and performing virtual
screenings to discover active compounds with the potential to
combat SARS
- Synthesizing and screening candidate drugs
- Performing anti-SARS tests
To date, SIMM researchers have created 3D models of several SARS proteins
and have already performed several virtual screenings utilizing numerous
databases of potential drug compounds.
The backbone of this research is a 64-processor SGI® Origin®
3800 supercomputer, an additional four-processor SGI® Origin®
3200 server and 15 SGI graphics workstations used to model and virtually
screen several million structures with the goal of developing a
new compound to combat the SARS virus. The Origin® server handles
data-intensive virtual screening tasks and the storage of many huge
chemical databases, both of which require the shared memory and
scalability of the Origin family's OpenGL® application programming
interface and NUMAflexTM technologies. To
address the SARS virus' characteristic mutation, the supercomputer
is being used to map mutation sites and to create data sets pinpointing
the structure of mutant proteins. Researchers utilize their SGI
graphics workstations to create 3D models of these protein structures
and to analyze the virtual screening results in real time.
SIMM, a branch of the Chinese Academy of Sciences, focuses on
discovering new drugs and drug candidates through an interdisciplinary
mix of such fields as biology, computer science, molecular biology,
informatics and computer-aided drug design.
"Our approach to the pressing need for SARS research is high-throughput
virtual screening integrated with chemistry and pharmacology," explains
Dr. Jiang Hualiang, head of a key SARS research team at SIMM. "We
are hoping within the next three months to find strong candidate
compounds that may potentially kill the SARS virus. The SGI Origin
supercomputer is incredibly powerful and stable, a must for such
tasks as parallel computation, which is critical in reducing screening
time. Our SGI workstations provide crucial visualization capabilities
for constructing 3D models."
The esteemed Beijing Genomics Institute, a member of the International
Human Genome Project Consortium best known for its important work
in the sequencing of the rice genome, was founded in 1999. BGI researchers
are fast at work sequencing 100 isolates of SARS in order to study
the multitude of variations of this unusually mutative virus. In
addition, diagnostic kits, vaccine and drug solutions are under
rapid development.
BGI, the largest nonprofit genomics research institute in the
Asia Pacific region and the third-largest genomics research center
in the world, relies on two 32-processor SGI® Origin®
3000 supercomputers, a 5TB SGI® TP9100 Fibre Channel storage
system and several Silicon Graphics® O2® graphics systems.
These technologies are being used for such vital tasks as the modeling
of both the genomic basis of SARS and SARS-related protein sequences,
along with a variety of intensive computational applications.
"The institute's threefold mission is to sequence genomes of all
kinds, particularly agricultural-related genomes, to advance the
study of DNA, RNA, protein structures and bioinformatics and to
conduct research on human health-related issues, including not only
the current SARS initiative but also genotyping and antibody-antigen
studies," says Dr. Wang Jun, who heads the BGI's Beijing campus
and its bioinformatics department. "All of these goals present huge
high-performance computing demands, especially in the areas of comparative
studies and genome-related analysis. Our SGI infrastructure uniquely
meets our large and very complex HPC and graphics challenges."
"We are honored that SIMM and BGI, two world-renowned institutes
conducting valuable research into a devastating disease, are using
SGI products to accelerate insight and discovery," said SGI CEO
and Chairman Bob Bishop. "Many other advanced laboratories are doing
the same, because SGI understands the urgency of leading-edge science
and of the breakthrough thinking that is needed to succeed."

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