Cray Inc., LION bioscience, KOOPrime and APBioNet Engineers Provide a Recipe for Bioinformatics; Working Toward An Integrated Data-Compute-Workflow Platform.Business Editors/High-Tech Writers SINGAPORE--(BUSINESS WIRE)--June 20, 2002 The Asia Pacific Bioinformatics Network (APBioNet) which promotes the growth of bioinformatics in the Asia Pacific region, has identified one of the biggest obstacles to widespread adoption amongst life scientists as the lack of integration and interoperability amongst the disparate bioinformatics software vendors, database providers and instrument devices. As a testbed pilot project, APBioNet is pleased to announce that it is currently working with the best of breed bioinformatics database provider LION bioscience (Neuer Markt: LIO, WKN WKN Wertpapier-Kenn-Nummer (identifying number assigned to securities traded in Germany) WKN Warrior Knowledge Network (US Army) 504 350) (Nasdaq:LEON) to integrate their popular SRS SRS, SRS-A see slow-reacting substance. system with supercomputing pioneer Cray Inc. (Nasdaq:CRAY) through the use of KOOPrime's applications integration system. Said Dr. Tin Wee Tan, APBioNet secretariat and cofounder co·found tr.v. co·found·ed, co·found·ing, co·founds To establish or found in concert with another or others. co·found , "To our bioinformatics user community, we have moved from command-line interfaces to nice but tedious GUIs, to repetitive Web form-filling and back. What we need is a protocol-based recipe system which biologists are familiar with, that allows us to stitch together things we do repeatedly, and to schedule and automate the workflow processes we have to grapple with to enter into contest with, resolutely and courageously. See also: Grapple daily." KOOPrime's applications integration system allows users to integrate data handling and instrument control from laboratory devices with database access and computational analysis. Until now, the database component and compute integration has been on an ad hoc For this purpose. Meaning "to this" in Latin, it refers to dealing with special situations as they occur rather than functions that are repeated on a regular basis. See ad hoc query and ad hoc mode. basis, and restricted to an enterprise-wide framework. By combining technologies from KOOPrime, LION bioscience and Cray Inc. and operating an Internet-wide bioinformatics workflow applications integration testbed, APBioNet aims to pioneer the concept of privately reusable, publicly contributed workflows and objects that can facilitate the seamless flow of data from devices to databases and computation servers across the Internet. This will help ease the problem with the integration of non-interoperable systems. Said the Chief Architect of LION bioscience's SRS, Dr. Thure Etzold: "We are pleased to cooperate with APBioNet, and will work towards unleashing the comprehensive spectrum of biological databases our ubiquitous SRS system provides, into the workflows which every bioinformaticist currently carries out either manually or through time-consuming scripting." "Automated device data gathering and complex database operations are incomplete without high performance compute power. Cray Inc. has previously worked with the APBioNet to launch a BioCray grid computing grid computing, the concurrent application of the processing and data storage resources of many computers in a network to a single problem. It also can be used for load balancing as well as high availability by employing multiple computers—typically personal network and with the National University of Singapore The National University of Singapore (Abbreviation: NUS) is Singapore's oldest university. It is the largest university in the country in terms of student enrollment and curriculum offered. to build Cray Bioinformatics Libraries," said Dick Russell, vice president of Cray Inc. "We now want to have that deeper integration with the biologist's workflow which includes data acquisition, database searching, and computation. Our role is to make the computational time transparent to the user so that they don't have to worry about it." Describing how the integration works, KOOPrime's 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. T.S. Lim explains, "We provide the platform for treating each step of a complex series of activities a biologist or bioinformaticist carries out as a `bubble.' By linking the output of one bubble to the input of the next bubble in a user-friendly manner, we can assemble complex workflows of bubbles and links." In this collaboration, KOOP bubbles are now built to wrap around SRS databases and the computational biology Not to be confused with Biologically-inspired computing. Computational biology is an interdisciplinary field that applies the techniques of computer science, applied mathematics, and statistics to address problems inspired by biology. applications running on Cray supercomputers that are part of computational grids like APBioGrid. "We are pleased that APBioNet is extending our enterprise system across the Internet," Lim added. "And it will allow participating users to write their bubbles and share their workflows with each other." "My biggest challenge is probably how to get people to build workflows and share them with each other," said Dr. Tan, who conceived the idea and is currently coordinating the whole project. "We already have a set of more than 200 bubbles, including 160 from the EMBOSS em·boss tr.v. em·bossed, em·boss·ing, em·boss·es 1. To mold or carve in relief: emboss a design on a coin. 2. suite, 40 from PHYLIP PHYLIP Phylogeny Inference Package (genetics software) , 20 Unix utilities This is a list of UNIX utilities as specified by IEEE Std 1003.1-2004, which is part of the Single UNIX Specification (SUS). These utilities can be found on UNIX Operating systems and most UNIX-like operating systems. List IEEE Std 1003. , a dozen from MySQL, a few for Globus Grid, BLAST, FASTA FASTA Fraternidad de Agrupaciones Santo Tomás de Aquino (Spanish: Fraternity of St Thomas Aquinas Groups ) FASTA Federal Acquisition Streamlining Act FASTA Fresno Area Substitute Teachers Association and CLUSTALW. Linking up with Cray Inc. and LION bioscience will help increase the power of this new workflow paradigm. It will shift the one-biologist one-workbench thought pattern to that of virtual Internet-wide, automated, shareable and reusable processes." About LION bioscience AG LION bioscience (Neuer Markt: LIO, WKN 504 350; Nasdaq: LEON) provides proven information and knowledge management solutions to significantly improve life science R&D performance and productivity. Founded in 1997, LION has more than 485 employees, with headquarters in Heidelberg, Germany, and subsidiaries in Cambridge, UK, Cambridge, Mass., and San Diego San Diego (săn dēā`gō), city (1990 pop. 1,110,549), seat of San Diego co., S Calif., on San Diego Bay; inc. 1850. San Diego includes the unincorporated communities of La Jolla and Spring Valley. Coronado is across the bay. , Calif. LION has partnerships with Aventis, Bayer, Boehringer Ingelheim, Celera, DuPont, GlaxoSmithKline, Janssen, Merck Inc., Nestle Novartis, Paradigm Genetics, Pharmacia & Upjohn, Roche, Sumitomo Pharmaceuticals and Tripos. About Cray Inc. (NASDAQ NM: CRAY) 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. About KOOPrime KOOPrime Pte Ltd PTE LTD Private Limited is one of the first software companies providing Enterprise Application Integration services and products to the life sciences industry. Founded in 2000 as a spin-off company from the National University of Singapore, the company focuses on allowing seamless and transparent flow of data and information from one component to another, resulting in business flows that can be visually personalized and automated by end users. About APBioNet The Asia Pacific Bioinformatics Network (APBioNet) is a non-profit, non-governmental, international organization founded in 1998. It focuses on the promotion of bioinformatics in the Asia Pacific Region. APBioNet has more than 20 organizational and 400 individual members from 12 countries in the Asia Pacific region. More about APBioNet can be found at: http://www.apbionet.org/. |
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