Bioinformatics Tools Cutting Cost & Time for Drug Discovery

According to a new research report – “Global Bioinformatics Market Outlook”- by RNCOS, the worldwide bioinformatics industry has seen a double-digit growth rate in the past few years and is forecasted to record a stupendous CAGR of 16.3% from 2007 to 2010.

The report says that the pressure of developing new drugs is intensifying on the global drug industry as existing drugs will go off-patent soon and costs of R&D are escalating sharply, making the companies to switch to bioinformatics. Therefore, the global bioinformatics industry will be led by increasing outlay on obtaining the bioinformatics tools and services by pharmaceutical and biotechnology companies to accelerate their drug discovery process.

Currently, the report says, an average drug takes approximately 10 years to reach clinical phase from the discovery phase and costs between US$ 400 Million and over US$ 1 Billion to the company, with much of the spending incurred at the final stages of the development. However, this huge cost of the drug development process can be cut down substantially by using bioinformatics and Computer-Aided Drug Design. For instance, the application of bioinformatics in the discovery and development of some new drug may reduce the annual cost and time by 33% and 30% respectively.

Other than cost and time benefit, blending of IT and life sciences, on one side, is helping the pharma companies to successfully overcome the challenges faced in collecting, processing, storing and analyzing data during the drug development process, and on the other side, pushing up the bioinformatics market, says the RNCOS research.

However, as the industry is at a nascent stage in most parts of the world, the market growth is hard to predict but it will certainly grow at a double-digit rate by 2010.

The report gives an exhaustive account on the global bioinformatics industry and provides forecast on its various segments, including drug patent expirations, bioinformatics market by segment, analysis software & service market, analysis software & service market by application, IT infrastructure & other services market, and drug delivery market.

“Global Bioinformatics Market Outlook” gives updated and detailed information on the industry and examines the emerging market trends. It offers an insight into the market and examines the bioinformatics market in major countries.

For more information visit: http://rncos.com/Report/IM554.htm
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New BoostServe™ Extreme Provides 1000x Acceleration for Selected Bioinformatics Applications

Redwood City, CA & Singapore – Progeniq Pte Ltd, a leader in providing accelerated computing solutions, today launched the BoostServe™ Extreme for the Bioinformatics industry. The product gives servers and desktops processing power equivalent to over one thousand CPU cores in less than one tenth the space of a server rack.

“The BoostServe™ Extreme launch is a major milestone in Progeniq’s aggressive R&D effort, delivering high-end, accelerated solutions for mid-sized research institutes at an unbeatable space and power footprint” said Progeniq’s VP Business Development, Mr. Teck Hiong Chua. “Other solutions in the market require at least one rack (42U) of server space to deliver 1,024 CPU cores of performance. The BoostServe™ Extreme provides a 1,000 CPU equivalent performance in just a tenth of that space. By installing 10 chained BoostServe™ units, the overall solution can scale linearly by ten times to 10,000 CPU core performance in each rack of datacenter space, presenting unprecedented scalability.”

BoostServe™ Extreme accelerates computationally intensive Bioinformatics applications like Smith-Waterman, ClustalW, HMMsearch, and HMMpfam, over one thousand times faster than a single CPU core. It consumes six hundred times less power, and slashes equivalent performance acquisition cost by 90%. Annual maintenance cost is estimated to be 80% lower than if the same performance had been achieved by CPUs alone.

Indian IVD Emerging as One of the Fastest Growing Segments

Advances in human genomics, bioinformatics, miniaturization, and microelectronics often blended with information and computer technology have led to a growth spurt in the global market for in vitro diagnostic (IVD) tests. Among others, Indian IVD market is anticipated to grow at a CAGR of around 15% during 2009-2012, emerging as Asia’s third largest IVD market after Japan and China, says our econometric study “Global In Vitro Diagnostic Market Analysis”. This growth rate compares with a CAGR of around 9% in the global IVD market during the same period.

We have done extensive research on the global IVD market in order to monitor various trends and developments undergoing across the key IVD markets. We have found that although Indian IVD market is very small compared to the global IVD market, it is growing at a rapid pace to outperform other major markets in near future. “Various factors, such as increasing urbanization, unhealthy diets and growing sedentary lifestyle, have strongly boosted the prevalence of lifestyle-related diseases such as diabetes and cardiovascular diseases in the country. Owing to these factors Indian IVD market is projected to grow at double the pace of the global IVD market,” says a research analyst at RNCOS.

We have observed that growing health consciousness among middle- and high-income families in India is heralding a new business opportunity. This has shifted focus from in-patient treatment to a regular preventive health check. For example, corporate companies offer annual health check for their employees, insurance companies conduct pre-insurance policy check, and self paid health checks also give out a potential business opportunity.

Our study analyzes the key markets and segments of Industry to give a brief about the future scenario of the industry. The technological factors driving the growth are improving techniques, lab automation process, improved data delivery system, etc. According to our industry experts, several steps should be taken by IVD manufacturers to invest in dedicated research and development.

“Global In Vitro Diagnostic Market Analysis” includes detailed analysis of the factors which are fueling the growth of Indian IVD market. Besides this, report also provides rational analysis and forecast on various segments and sectors of the industry.

For FREE SAMPLE of this report visit: http://www.rncos.com/Report/IM103.htm

Check DISCOUNTED REPORTS on: http://www.rncos.com
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About RNCOS:

RNCOS, incorporated in the year 2002, is an industry research firm. We are a team of industry experts who analyze data collected from credible sources. We provide industry insights and analysis that helps corporations to take timely and accurate business decision in today’s globally competitive environment.

H1N1 Influenza A1 Virus & Bioinformatics

1. Dr Sebastian Maurer-Stroh and his team of scientists from A*STAR’s
Bioinformatics Institute (BII) have become the first in the world to demonstrate how
bioinformatics and computational biology can contribute towards managing the H1N1
influenza A1 virus. They published their complex analysis, entitled, “Mapping the
sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to
drug and antibody binding sites”, in Biology Direct, a peer-reviewed journal on 20
May 2009.
2. In this paper, Dr Maurer-Stroh and his group showed the evolutionary analysis
of a critical protein produced by the 2009 H1N1 influenza A virus strain –
neuraminidase – as well as demonstrated the use of a computational 3-dimensional
(3D) structural model of the protein. With the model they developed, Dr Maurer-
Stroh and his team were able to map the regions of the protein that have mutated
and determine if drugs and vaccines that target specific regions of the protein were
effective. The team unveiled interesting discoveries such as the following:
a. the neuraminidase structure of the 2009 H1N1 influenza A virus has
undergone extensive surface mutations compared to closely related
strains eg, the H5N1 avian flu virus or other H1N1 strains such as the
1918 Spanish flu;
1 Influenza A virus strains are categorized according to two proteins found on the surface of the virus:
haemagglutinin (H) and neuraminidase (N). All influenza A viruses contain haemagglutinin and
neuraminidase. The structures of these proteins differ from strain to strain eg, swine flu belongs to the
H1N1 type, avian flu to H5N1 and the currently dominant seasonal flu belongs to the H3N2 type.
b. the neuraminidase of the 2009 H1N1 influenza A virus strain is more
similar to the H5N1 avian flu than to the historic 1918 H1N1 strain
(Spanish flu);
c. the current mutations of the virus have rendered previous flu
vaccinations directed against neuraminidase less effective; and
d. the commercial drugs, namely Tamiflu® and Relenza®, are still
effective in treating the current H1N1 virus.
3. Said Dr Frank Eisenhaber, Director of BII, “BII’s H1N1 virus sequence study
marks a significant milestone in the use of computational biology methods in
understanding how the mutations of the fast evolving influenza virus affect
immunogenic properties or drug response. This information helps to develop a
strategy for fighting the H1N1 virus and for organising an effective treatment for
patients.”
Findings published in record time
4. Equally significant is the speed at which the paper was published – in a mere
two weeks from the time the first patient virus samples were made available. Dr
Sebastian Maurer-Stroh, Principal Investigator at BII and first author of the paper,
said, “Because we were working as a team, driven by the common goal to
understand potential risks from this new virus, our group at BII was able to
successfully complete this difficult analysis within such a short time”.
Other technologies against H1N1 virus
5. Besides this powerful 3D model by BII, A*STAR scientists have also
developed other technologies to tackle the 2009 H1N1 Influenza A virus. They
include:
a. a chip2 that is able to quickly sequence or decode the genes in the flu
virus and distinguish between the H1N1, seasonal, and mutated flu
strains;
b. a microkit3 for the detection and identification of the flu virus strain
within 2 hours; and
2
This chip has been developed by scientists at the Genome Institute of Singapore (GIS).
c. a molecular diagnostic assay4 to

Chinese National Human Genome Center at Shanghai Leverages Accelerated Bioinformatics Solution from SGI and Mitrionics for Faster Time to Insight

To help extinguish effects of the ancient parasite, the Schistosoma japonicum or blood fluke – one of the major infectious parasites to a wide range of hosts including primates, rodents, carnivores, and humans — Chinese Scientists at the China National Human Genome Center (CHGC) in Shanghai are using SGI (NASDAQ: SGIC) compute technology running a Mitrion-accelerated bioinformatics application to improve early disease diagnosis and discover new drugs to effectively treat disease caused by this parasite.

Blood fluke has evolved for thousands of years. Currently, existing drugs target disease caused by blood fluke found in South America. In the past few years the Schistosoma japonicum has been re-found in some lakes and rivers in the east and south China area. To study the parasite evolution, improve disease diagnosis in the very early stages, and develop more effective drugs to treat disease, Chinese bioscientists decided to discover the secrets of the blood fluke genome.

CHGC implemented the first phase of blood fluke genomics sequencing using the new SGI® RASC™ Appliance and SGI InfiniteStorage 350 storage solution, installed in February. CHGC bioscientists achieved faster query times — up to 10 times faster — with the combination of SGI RASC (Reconfigurable Application-Specific Computing) technology, an accelerated version of BLAST-n software developed by Mitrionics, and the acclaimed SGI® Altix® server platform.

SGI® InfiniteStorage 350 ensures that the data generated by the CHGC research is both protected and available to maximize analysis. A cost effective solution, the initial purchase of 8TB allows plenty of capacity for future expansion as the need arises. With integrated controllers, the density of the SGI InfiniteStorage 350 contributes to the mobility of Bioinformatics solution.

“Shortened time to results is critical to our success. With the blood fluke genome research, we have 300 million base pairs to study, and have 6-7 times more calculations in each step. The large shared memory and ease-of-use with the SGI RASC Appliance for BioInformatics enables our scientists to focus on achieving results faster and not spending valuable time on computer science,” said Dr.Zhou, Deputy Director of Bioinformatics Department, CHGC.

The SGI RASC Appliance for Bioinformatics is a pre-configured solution that dramatically simplifies nucleotide sequence queries using BLAST-n. The industrial-scale appliance addresses productivity problems in a range of bioinformatics environments — from those that serve thousands of users running BLAST queries against a single database, to others with smaller numbers of users running complex queries against databases that are hundreds of Gigabytes in size.

Using Mitrionics software and an accelerated version of NCBI BLAST-n, the SGI RASC Appliance for BioInformatics offloads genome sequencing workloads that typically run on Linux® clusters. The Mitrion accelerated BLAST-n running on the SGI RASC Appliance for BioInformatics runs large queries up to 15 times faster than a single-core r nodes powered by AMD Opteron 8820 SE processors, and production runs of thousands of smaller queries by up to 60 times faster.

The SGI RASC Appliance for BioInformatics further increases throughput by executing multiple BLAST-n queries in parallel on multiple FPGAs. With up to 16 FPGAs in a single SGI RASC Appliance for BioInformatics, customers can achieve throughput equal to between 240 and 960 AMD Opteron cores without the solution complexity and system management overhead.

“The accelerating pace of genomics research means scientists are running more and larger sequence queries. The turnkey solution SGI and Mitrionics have developed makes the genomics sequencing faster and easier, and the power consumption per BLAST-n query is as little as one-tenth,” said Alex Lee, country manager of SGI Greater China Region. “CHGC’s successful implementation of this solution is tantamount to their leadership position in China and the world.”

“This turnkey accelerated BLAST solution from Mitrionics and SGI represents a significant HPC industry milestone by establishing new performance levels for processing power and reduced power consumption,” stated Anders Dellson, CEO of Mitrionics, Inc. “Bioinformatics and genomics are among the areas in the life sciences industry where several of the most widely-used applications are ideally suited for FPGA acceleration. We’re extremely excited to be working with both SGI and CHGC as they are leading their respective industries in delivering and utilizing accelerated computing technologies.”

The CHGC also recognized that the research into the genome of the blood fluke would require them to run much more than BLAST-n. The scalable, general purpose nature of the SGI RASC Appliance for BioInformatics supported that capability by enabling the system to be upgraded to a total of 48-cores of Intel® Itanium® 2 processors, 128GB of shared memory and an InfiniteStorage 350 with 8TB of disk storage. The system’s ease-of-use and portability of open source software running in the shared memory environment have proved crucial for the second phase of their research. The SGI RASC Appliance for BioInformatics is running Novell’s SUSE® Linux® Enterprise Server 10. A CHGC research paper is scheduled to be published in July.

About CHGC
Chinese National Human Genome Center at Shanghai (CHGC), a new research unit organized by the institutes from the related fields in Shanghai for fulfilling the national scientific projects of human genome research and its application and development, was established on October. 29th,1998 on the basis of its former Shanghai Human Genome Center founded in Shanghai Pudong Zhang-Jiang High-tech Park on March 4th, 1998.

The founding members of CHGC include National Center for Biotechnology Development affiliated to Chinese Ministry of Science and Technology, Shanghai New Drug Research and Development Center, Pudong Technical Venture Capital Company, Shanghai Branch of Chinese Academy of Sciences, Fudan University, Ruijin Hospital affiliated to Shanghai Second Medical University, Shanghai Institute of Cancer Research, Shanghai Medical University, Shanghai Second Military Medical University, and Shanghai Zhang-jiang Hi-Tech Park Development Company. www.chgc.sh.cn

About Mitrionics
Founded in 2001, Mitrionics, Inc. is the technology leader in the exciting new field of FPGA Supercomputing which provides higher processing power and lower energy consumption than clusters of computer systems. The company’s Mitrion Virtual Processor and Mitrion Software Development Kit provide cost effective FPGA Supercomputing power to organizations for their most critical applications. The Mitrion Platform is unique from any other FPGA programming solution, because it eliminates the need for circuit design skills, thus making FPGA Supercomputing performance accessible to an entire new market of scientists and developers. Mitrionics has key industry relationships with Cray, Nallatech, and Silicon Graphics. For more information, visit the company Web site at www.mitrionics.com, or call 310-558-9495, or email: info@mitrionics.com.

SGI – Innovation for Results™
SGI (NASDAQ: SGIC), is a leader in high-performance computing. SGI delivers a complete range of high-performance server and storage solutions along with industry-leading professional services and support that enable its customers to overcome the challenges of complex data-intensive workflows and accelerate breakthrough discoveries, innovation and information transformation. SGI solutions help customers solve their computing challenges whether it’s enhancing the quality of life through drug research, designing and manufacturing safer and more efficient cars and airplanes, studying global climate, providing technologies for homeland security and defense, or helping enterprises manage large data. With offices worldwide, the company is headquartered in Sunnyvale, Calif., and can be found on the Web at www.sgi.com.

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