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Computing Power for the Post-Genomic Era

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Computing Power for the Post-Genomic Era January 2002 Life Sciences Group Compaq Computer Corporation Contents Compaq Computer DEFINITIONS........................................... 3 Life Science Program LIFE SCIENCE INDUSTRY OVERVIEW .............................................. 3 Abstract: COMPAQ’S MARKET POSITION: This document presents an overview of Compaq in the Life Science NUMBER ONE IN LIFE SCIENCE discovery market. It includes a market overview, Compaq’s market DISCOVERY ............................................. 4 position, reference sites and collaborations, and a description of the CELERA GENOMICS ................................ 4 key components of Compaq’s solutions for Life Science discovery. THE WELLCOME TRUST SANGER INSTITUTE ............................................... 5 The benefits of Compaq’s solutions for the Life Science industry are THE WHITEHEAD INSTITUTE CENTER FOR discussed. GENOME RESEARCH ............................... 5 CENTRE NATIONAL DE SEQUENÇAGE (GENOSCOPE).......................................... 5 GENEPROT, INC. ..................................... 5 GENENTECH ............................................ 5 THE INSTITUTE FOR GENOMIC RESEARCH (TIGR) .................................................... 6 ENTELOS ................................................. 6 ACADEMIA SINICA................................ 6 STRUCTURAL GENOMIX......................... 6 PITTSBURGH SUPERCOMPUTING CENTER (PSC) ...................................................... 6 COMPAQ MARKET POSITION: NUMBER ONE IN HPTC........................ 7 COMPUTING POWER FOR THE POST-GENOMIC ERA............................ 7 COMPAQ BIOCLUSTER............................ 8 COMPAQ LIFE SCIENCE INVESTMENT PROGRAM................................................ 8 COMPAQ’S LIFE SCIENCES SOLUTIONS.............................................. 9 FULL RANGE OF HIGH-PERFORMANCE COMPUTING SYSTEMS ............................ 9 TODAY: THE BEST ABSOLUTE PERFORMANCE WITH ALPHASERVER SYSTEMS ................................................. 9 TOMORROW: THE COMPAQ/INTEL ANNOUNCEMENT ENHANCES COMPAQ’S HPTC ROADMAP AND SOLUTIONS....... 10 STORAGEWORKS TECHNOLOGY FOR HIGHLY RELIABLE, SCALABLE, MODULAR STORAGE SYSTEMS............. 11 APPLICATION PORTFOLIO..................... 11 PROFESSIONAL SERVICES............... 12 COMPAQ FINANCIAL SERVICES ............ 12 SUMMARY OF COMPAQ SOLUTION BENEFITS ............................................... 12 CONTACT INFORMATION................ 13 Notice Compaq Computer Corporation’s Life Science Program Document prepared by High Performance Technical Computing Group First Edition November 2001. The information in this publication is subject to change without notice and is provided “AS IS” WITHOUT WARRANTY OF ANY KIND. The entire risk arising out of the use of any information presented in this paper remains with the recipient. In no event shall Compaq e liable for any direct, consequential, incidental, special, punitive or other damages whatsoever (including without limitation, damages for loss of business profits, business interruptions of loss of using information), even if Compaq has been advised of the possibility of such damages. The limited warranties for Compaq products are exclusively set forth in the documentation accompanying such products. Nothing herein should be construed as constituting a further or additional warranty. This publication does not constitute an endorsement of the product or products that were tested. The configuration of configurations tested or described may or may not be the only available solution. This test is not a determination or product quality or correctness, nor does it ensure compliance with any federal, state, or local requirements. Product names mentioned herein may be trademarks and/or registered trademarks of their respective companies. Compaq, the Compaq logo, AlphaServer, NonStop, OpenVMS, ProLiant, StorageWorks, Tru64 and TruCluster are trademarks of Compaq Information Technologies Group L.P. in the U.S. and/or other countries. UNIX is a trademark of The Open Group. Intel and Itanium are trademarks or registered trademarks of Intel Corporation. Linux is a registered trademark of Linus Torvalds. Windows is a registered trademark of Microsoft Corporation. PhysioLab is a trademark of Entelos, Inc. All other product names mentioned herein may be trademarks or registered trademarks of their respective companies. Copyright © 2001,2002 Compaq Computer Corporation. All rights reserved. Definitions There are many definitions of Life Science. This paper focuses on the Life Science discovery sector: genomics, proteomics, functional genomics, comparative genomics, physiomics, systems biology, pathways and others. Life science is becoming increasingly quantitative as new technologies facilitate collection and analysis of vast amounts of data ranging from complete genomic sequences of organisms to three-dimensional protein structure and complete biological pathways. As a consequence, biomathematics, biostatistics and computational science are crucial technologies for the study of complex models of biological processes. High performance computing technology is a requirement for this industry and enables the study of complex models of these biological processes. Compaq Computer Corporation supplies high performance solutions for wide range of Life Sciences organizations and is a critical partner for researchers who are working to improve human health. Life Science Industry Overview There is no doubt that the sequencing and initial annotation of the human genome, completed in April 2001, is one of the great scientific advancements in history. There is also no question that this breakthrough in biological research was made possible by advances in high performance computing technology. High-speed computers are necessary to analyze the hundreds of terabytes of raw sequence data and correctly order the 3.2 billion base pairs of DNA that compose the human genome. Compaq is at the forefront of this technological breakthrough, providing the solutions required as companies, organizations and agencies open new and exciting chapters in life science. The staggering quantity and complexity of data generated by the Human Genome Mapping Project (HGMP) has created a huge demand for high performance computing. Genetic databases are estimated to double in size every six to eight months, more than twice as fast as Moore’s Law predictions for microprocessor performance improvements. Genomic research organizations such as Celera Genomics, the Whitehead Institute Center for Genome Research, and the Sanger Institute are already managing many terabytes of data, larger in size than the Library of Congress. That data will grow exponentially over the next several years. The computing resources required for the HGMP are millions of times greater than used to land a man on the moon. Today, separating the advances in biotechnology from advances in high performance computing is increasingly difficult. Many leading scientists believe that high-end computing is the future of biology and medicine. High performance computing has become the third leg of traditional scientific research, along with theory and experimentation. The assembly and initial annotation is only the first step on a long road to understanding the human genome. Many companies, research institutes, universities and government laboratories are now rapidly moving on to the next steps: comparative genomics, functional genomics, proteomics, pathways, systems biology and whole organ modeling. Researchers are beginning the quest to determine exactly how each gene and protein functions and, more important, how they malfunction to trigger deadly illnesses from heart disease and cancer to Alzheimer’s and Parkinson’s diseases. Increasingly powerful computers and software will be needed to gather, store, analyze, model and distribute information. The availability of the biological data, coupled with powerful software analysis tools and powerful computer systems, will allow scientists to develop new diagnostics, drug therapies and new strategies and methods for identifying disease genes and, eventually, personalizing medicine. In addition, agrochemical companies and traditional chemical companies are also investing in bioinformatics to develop new strains of seeds, herbicide resistant crops and novel biomaterials. Bioinformatics is a large part of the R&D investment that agrochem, chemical, pharmaceutical, and biotech companies are making today as they strive to develop and bring products to market faster. In addition, industry analysts estimate up to 100 percent annual revenue growth for genomics companies, while information technology spending is expected to match or exceed that rate. Computing companies, like Compaq, are responding with ever more powerful, faster, reliable and cost-effective computing solutions. Compaq’s Market Position: Number One in Life Science Discovery Compaq stands as the leading supplier of computing systems for Life Science research, according to International Data Corporation (IDC). Compaq works with many of the major research centers worldwide, including the world’s largest genomic sequencing facilities at Celera Genomics in the USA and the Wellcome Trust Sanger Institute in the United Kingdom. With Compaq working as a partner, the time to process the mapping of the full human genome was dramatically compressed through more aggressive and large- scale application of sequencing and computing technology. Most of the leading commercial and public genomics
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