Cray, LION bioscience & Partners Provide a Recipe for Bioinformatics

SINGAPORE -- 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 504 350) (Nasdaq:LEON) to integrate their popular SRS 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, "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 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 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 network and with the National University of Singapore 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 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 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 suite, 40 from PHYLIP, 20 Unix utilities, a dozen from MySQL, a few for Globus Grid, BLAST, FASTA 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."