SCIENCE AND ENGINEERING NEWS
Washington, DC, — The U.S. Department of Energy (DOE) announced today that Sandia National Laboratories and Celera Genomics (NYSE:CRA), an Applera Corporation business, have signed a Cooperative Research and Development Agreement. Compaq Computer Corporation (NYSE:CPQ) will provide the project technology. The goal of the project is to develop the next generation software and computer hardware solutions that will be specifically designed for the demands of computational biology as well as a full range of life sciences applications.
Celera and Sandia signed the agreement in a ceremony at the Department of Energy with Secretary of Energy Bill Richardson presiding. Celera, Sandia and Compaq will work together to increase computing capability with the goal of achieving 100 trillion operations per second (100 TeraOPS). By sharing some computing technology developed by Sandia, Celera and Compaq may ultimately reach the “petacruncher” (1,000 TeraOPS) level. This level of cooperation is necessary to meet the dramatic increases in performance required for emerging genomics and proteomics applications at affordable prices, and brings together the capabilities of three leaders in the fields of bioinformatics, high performance computing, and massively parallel systems.
Proteomics is the study of the function, structure and interactions of proteins in cells, including humans and other organisms. “The next stage of the biotechnology revolution that was started by the Human Genome Program will be fueled by the successful marriage of molecular biology with high performance computing science,” said Secretary Richardson. “The Department of Energy, as it helped develop the technology that made the human genome project possible, once again, is forging ahead to provide the tools to bring the genome to life.”
“The key aspect of this R&D relationship is the simultaneous provision of algorithmic support, design of actual application software, and development of the system platform by three organizations with world-class competence in their respective areas,” said Bill Blake, Vice President of High Performance Technical Computing at Compaq. “This effort is a direct response to the challenge by Celera’s president, J. Craig Venter, who said that even the most powerful of today’s supercomputers do not meet the needs of his company’s work in the genomic era. Our intent with this alliance is to apply the same full system modeling approach to bioscience that has been so successfully applied to physical sciences in the DOE/NNSA Stockpile Stewardship program.”
J. Craig Venter, Celera’s president and chief scientific officer, said, “Just three years ago, the computational needs of biology were thought to be minor and irrelevant to the computing industry. Today, biologists are setting the pace of development for the industry. At Celera, we take pride in excelling in the application of computers to biology and the new era in medicine that is developing as a result. As Compaq and the Department of Energy move toward creation of the next generation of supercomputers for defense purposes, we look forward to helping both groups develop the new machines, software and algorithms to advance life sciences.”
Said Bill Camp, Sandia director of computation, computers and mathematics, “Delivering affordable and scalable computer architectures is the foundation of modern supercomputing and has been the focus of Sandia research for more than a decade. Our knowledge will be useful because understanding the complexity of the human genome requires manipulating ever vaster amounts of information, using more advanced computing technologies than was required even for the assembly of the human genome itself. So we view this relationship as strategic for our continuing missions as a DOE/NNSA national security laboratory, look forward to providing world-class expertise in parallel algorithms and systems software in the cause of human health, and welcome the opportunity to play a role in developing what may be some of the most exciting science in recent human history.”
The alliance will use Compaq Alpha processors connected in massively parallel configuration with extremely high bandwidth, and low latency mesh interconnects. Compaq and Sandia will collaborate on the development of system hardware and software. Both have extensive experience with supercomputers based on Alpha.
Compaq already manufactures a line of supercomputers, the AlphaServer SC series, that was recently selected by the DOE’s National Nuclear Security Administration (NNSA) as the architecture for the world’s most powerful computer, the ASCI Q system, that will deliver 30 trillion operations per second when delivered in 2002. ASCI, the Accelerated Strategic Computing Initiative, is a key component of the Stockpile Stewardship program to ensure the safety and reliability of the nation’s nuclear weapons stockpile in the absence of nuclear testing.
Sandia currently operates the most powerful Linux-based supercomputer in existence, CplantTM, which employs more than 1600 Alpha processors. Sandia also is home to ASCI Red, the first TeraOp supercomputer, until very recently the fastest supercomputer in the world. The alliance will focus on future generations of the AlphaServer SC series, and the goal is to create a prototype in the 2004 time frame.
Celera and Sandia will concentrate on creation of advanced algorithms for biology research, and on new visualization technologies for analyzing the massive quantities of experimental data from high-throughput instruments. All three groups will contribute to integrating the system hardware and software and on optimizing performance.
Driving the design for this next-generation supercomputer are anticipated computational and data management requirements for proteomics. These requirements are expected to be vastly more complicated than the pattern recognition and assembly operations required to sequence the human genome. Researchers are counting on proteomics to take advantage of genomic databases in developing new medicines, crops, materials and solutions to challenges in energy development and environmental cleanup.
Compaq Computer Corporation, a Fortune Global 100 company, is the largest supplier of computing systems in the world. Compaq designs, develops, manufactures and markets hardware, software, solutions, and services, including industry-leading enterprise computing solutions, fault-tolerant business-critical solutions, and communications products, commercial desktop and portable products, and consumer PCs.
Compaq products and services are sold in more than 200 countries directly to businesses, through a network of authorized Compaq marketing partners, and directly to businesses and consumers through Compaq’s e-commerce Web site at http://www.compaq.com . Compaq markets its products and services primarily to customers from the business, home, government, and education sectors.
Applera Corporation, formerly PE Corporation, comprises two operating groups. The Celera Genomics Group, headquartered in Rockville, MD, intends to be the definitive source of genomic and related medical information. Celera has developed three business units: the On-line Information Business, Discovery Sciences, and Discovery Services, all of which build upon Celera’s generation, integration, and analysis of biological information. Celera intends to enable therapeutic discoveries both through its own application of its scientific capabilities and in partnership with pharmaceutical and biotechnology companies. The Applied Biosystems Group (NYSE:ABI) develops and markets instrument-based systems, reagents, software, and contract services to the life science industry and research community. Customers use these tools to analyze nucleic acids (DNA and RNA) and proteins in order to make scientific discoveries, develop new pharmaceuticals, and conduct standardized testing. Applied Biosystems is headquartered in Foster City, CA, and reported sales of $1.4 billion during fiscal 2000.
About Sandia National Laboratories
Sandia is a multiprogram DOE laboratory, operated by a subsidiary of Lockheed Martin Corp. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major research and development responsibilities in national security, energy, and environmental technologies.
Web site: http://www.sandia.gov
Web site: http://www.compaq.com
Web site: http://www.applera.com