Cray Inc., ZIB and Bielefeld University Collaborate On Advanced Bioinformatics Software Solutions.Business Editors & High-Tech Writers Projects Target Better Methods For EST EST electroshock therapy. EST abbr. electroshock therapy Clustering, Protein Database Searches and 3D Protein Structure Prediction Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry. Its aim is the prediction of the three-dimensional structure of proteins from their amino acid sequences, sometimes including additional relevant information such as , Using Special Features of Cray Supercomputers Cray Inc. (Nasdaq:CRAY) today announced it is collaborating with Germany's Konrad-Zuse-Zentrum fur Informationstechnik Berlin (ZIB) and Bielefeld University to develop advanced software solutions for tackling some of the most challenging problems in the burgeoning new field of bioinformatics: EST clustering, sensitive protein database searches, and three-dimensional protein structure prediction. Better solutions for these problems could accelerate understanding of the genetic bases of diseases and lead to more-effective drugs and medical treatments. The two-year agreement, effective immediately, will make Cray supercomputer expertise and advanced technologies accessible to collaborating scientists at Bielefeld University's Institute of Bioinformatics and ZIB's Division of Computer Science. The accessible technologies will include the current-generation Cray SV1(TM) and next-generation Cray SV2(TM) (code name) supercomputers, both employing powerful special features originally developed for the intelligence community--as well as cluster systems based on standard microprocessors. Initial results are expected by the end of 2002. According to according to prep. 1. As stated or indicated by; on the authority of: according to historians. 2. In keeping with: according to instructions. 3. Bart Mellenbergh, Cray's bioinformatics practice leader for Europe, the Middle East and Africa Europe, the Middle East and Africa, usually abbreviated to EMEA, is a regional designation used for government, marketing and business purposes. It is particularly common amongst North American based companies, who often divide their international operations into the , the agreement covers three main initiatives: -- New algorithms (mathematical formulas) for EST clustering. A team led by Dr. Jens Stoye, head of Genome Informatics (Genominformatik) at Bielefeld University, will collaborate in creating new algorithms for EST clustering. EST (Expressed Sequence Tag) clustering is an established method for determining which genes are expressed in a given cell. The targeted algorithms will address exclusion methods (which genes do not belong to the cell) and verification of non-excluded genes--a task usually done today with some variant of a Smith-Waterman algorithm. -- New algorithms for sequence alignment. Determining the function of proteins is one of the most fundamental challenges in genomic research, and function is related to structure. If information on a protein's structure is unavailable, as is often the case, comparisons are made with members of the same protein family. The new "jumping alignment" method has been proven superior to established methods, but its computational complexity has prohibited its use in large-scale database searches. Dr. Stoye will pursue the development of new algorithms that make the jumping alignment method practical by exploiting the special hardware features residing in Cray SV-series supercomputers. -- New algorithms for three-dimensional protein structure prediction. There is still a huge gap between the number of known protein (DNA) sequences and the number of known 3-D structures of proteins. Accurate 3-D structure prediction of proteins based on sequence information is one of the "grand challenge" problems of bioinformatics. Dr. Thomas Steinke of ZIB's Division of Computer Science will lead the initiative to create more-effective algorithms that exploit information from atomistic (molecular dynamics) simulations using classical force fields and/or improved potentials based on quantum chemical data. Once again, the special capabilities of the Cray SV-series supercomputers are expected to make the development and use of these algorithms feasible. "Validation and benchmarking of algorithmic approaches under development for the simulation of biomolecular systems require a well-balanced computer architecture. Especially, the expected sustained processor-memory bandwidth on the Cray SV2(TM) system is indispensable for our planned simulations. We are highly pleased and looking forward to making a substantial step towards more complex molecular scenarios," said Dr. Steinke. According to Dr. Stoye, "This collaboration gives us the unique possibility to apply our algorithms in a high-end computational environment. We expect this to result in more powerful tools for the practical bioinformatics community." "Jens Stoye and his Bielefeld University colleagues have had outstanding success in developing effective new bioinformatics algorithms, with a focus on methods for pairwise and multiple sequence comparisons," said Cray's Mellenbergh. "Thomas Steinke and his group at ZIB have long experience in contributing to the development of quantum chemical production codes, including optimizing and parallelizing To generate instructions for a parallel processing computer. applications in the area of molecular simulations." Mellenbergh said ZIB currently operates a 544-processor Cray T3E The Cray T3E was Cray Research's second-generation massively parallel supercomputer architecture, launched in 1995. Like the previous Cray T3D It was a fully distributed memory machine using a 3D torus topology interconnection network. (TM) massively parallel See MPP. supercomputer and a 16-processor Cray J90(TM) vector computer. "We are excited to be working with individuals and institutions of this high caliber on initiatives with the potential to benefit science and the quality of human life," said Cray Chairman and CEO (1) (Chief Executive Officer) The highest individual in command of an organization. Typically the president of the company, the CEO reports to the Chairman of the Board. James Rottsolk. "Cray is fully committed (Law) committed to prison for trial, in distinction from being detained for examination. See also: Fully to the ambitious goals of this collaboration with ZIB and Bielefeld University." About the Konrad-Zuse-Zentrum fur Informationstechnik Berlin The Konrad-Zuse-Zentrum fur Informationstechnik Berlin (Konrad Zuse (person) Konrad Zuse - The designer of the first programming language, Plankalkül, and the first fully functional program-controlled electromechanical digital computer in the world, the Z3. He died on 1995-12-18 in Huenfeld, Germany. Biography. Center for Information Technology) helps to solve crucial problems in science, technology, environment and society, problems that cannot be solved by traditional methods but are accessible to mathematical analysis Analysis has its beginnings in the rigorous formulation of calculus. It is the branch of mathematics most explicitly concerned with the notion of a limit, whether the limit of a sequence or the limit of a function. . Founded in 1984 as a non-university research institute of the State of Berlin, ZIB collaborates closely with universities and scientific institutes in Berlin, and offers access to high-performance computers. ZIB also conducts joint projects in telecommunications, medical sciences, public transportation and logistics, the chemical, electrical, computer, and automotive industries Automotive Industries, Ltd. (Hebrew: תעשיות רכב נצרת עלית, תע"ר , as well as mechanical engineering. About Bielefeld University Bielefeld University (Universitaet Bielefeld) combines the best German university tradition with innovative research and teaching structures. Complementary to the university's 14 faculties is the Interdisciplinary Center The Interdisciplinary Center (IDC) (Hebrew: המרכז הבינתחומי) is a private college located in Herzlia, Israel. for Biotechnology (CeBiTec) that includes, among others, the International Graduate School in Bioinformatics and Genome Research Genome Research is the title of a peer-reviewed scientific journal published by Cold Spring Harbor Laboratory Press. The focus of the journal is on genome-wide studies in any organism, including single gene studies that are placed in a genomic context. , established with a grant from the Ministry of Education and Research of the state of North Rhine-Westphalia North Rhine–Westphalia (nôrth rīn-wĕstfāl`yə), Ger. Nordrhein-Westfalen (nôrt`rīn-vĕst'fä`lən), state (1994 pop. 17,759,000), 13,111 sq mi (33,957 sq km), W central Germany. . Within the CeBiTec, the new Institute of Bioinformatics began operating in the spring of 2002. About Cray Inc. Cray is the premier provider of supercomputing solutions for customers' most challenging scientific and engineering problems. Go to www.cray.com for more information about the company. Safe Harbor Safe Harbor 1. A legal provision to reduce or eliminate liability as long as good faith is demonstrated. 2. A form of shark repellent implemented by a target company acquiring a business that is so poorly regulated that the target itself is less attractive. Statement This press release contains forward-looking statements forward-looking statement A projected financial statement based on management expectations. A forward-looking statement involves risks with regard to the accuracy of assumptions underlying the projections. . There are certain factors that could cause Cray's execution plans to differ materially from those anticipated by the statements above. Among these factors are the technical challenges of developing new high performance computer systems, government support for supercomputer development and sales, sales risks for current and new supercomputer systems Three firms have held, simultaneously, the name Supercomputer Systems or Supercomputing Systems. The first was founded by Steve Chen, architect of the Cray X-MP and Cray Y-MP. The second was based in San Diego, California, USA. , expected delivery and acceptance times, the timely availability of necessary components from third parties that meet Cray's specifications, the ability of Cray supercomputer systems to pass individual customer acceptance tests and general economic and market conditions. Cray is a registered trademark, and Cray T3E, Cray J90, Cray SV1 and Cray SV2 are trademarks, of Cray Inc. All other trademarks are the property of their respective owners. |
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