HPCwire: Swami, the Next Generation Biology Workbench

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October 28, 2005

Swami, the Next Generation Biology Workbench

by Lynne Friedmann, Science Writer for SDSC

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A free, web-based interface that links molecular biology databases with analysis programs -- accessed thousands of times a week by scientists and students worldwide -- is about to become even better.

In May, the San Diego Supercomputer Center at UC San Diego announced the award of $2.2 million from the National Institutes of Health to build on the ground-breaking "Biology Workbench." Introduced by pioneering bioinformatics researcher Shankar Subramaniam nearly a decade ago, Workbench provides broad access to many biology software tools and data resources through a web-based, point-and-click computational environment. The offering also delivers the advantage of speed, letting researchers complete within hours work that once took days or even months.

The Next Generation Biology Workbench (NGBW), also known as Swami, is a versatile biological analysis environment that lets users search up-to-date protein and nucleic acid sequence databases. Searching is integrated with access to a variety of analysis and modeling tools -- all within a point-and-click interface that eliminates file format compatibility problems. This has made the Workbench an indispensable resource for scientists who work in bioinformatics, an emerging discipline in which researchers collect, integrate, model and analyze the explosion of biological data produced by such efforts as the Human Genome Project.

In addition to adding to fundamental scientific knowledge, this research can lead to improved understanding of disease and open the door to development of new treatments and drug discovery. The NGBW prototype, as well as links to the current Biology Workbench can be found at http://www.ngbw.org.

"I have been using Biology Workbench on a regular basis for the last three to four years," said Vanderbilt University assistant professor Mark de Caestecker. "It has proved to be an invaluable tool for the analysis and design of gene and protein constructs used in a range of different experiments in my laboratory. The Biology Workbench has the most comprehensive and easy-to-use applications I have come across." In his research, de Caestecker studies stem cell differentiation in kidney development, cancer, and tissue injury repair, and also researches cellular signaling in relation to hypertension.

Researchers are making Biology Workbench even more useful by expanding its present offering of 65 tools. Like the original, NGBW will continue as a free web resource that offers access to data, data storage, software tools and computational resources that help researchers mine the information in many popular protein and nucleic acid sequence databases. NIH funding will support the construction of up-to-date features such as improved user interfaces and an expandable architecture that will allow the NGBW to continue to evolve in the future in response to new developments in technology, biology and the needs of scientists.

"There have been huge leaps in the technologies used in building cyberinfrastructure since the original Biology Workbench was created," said Mark A. Miller, SDSC project leader for the new grant.

Work will be done in phases with a beta release planned for April 2006. According to Miller, there are some upgrades that can be accomplished in a matter of months, while others will take a year or two to accomplish. For example, the current workbench integrates information from 33 public databases, which are downloaded into a flat file. Using the less powerful technology of the flat file format places significant limitations on search functionality. Therefore, a major goal of the Next Generation project is to adopt a relational database format in which the information is broken down into tables and categories, which then allows more complex queries, or scientific questions, to be answered.

"Software developers always want to make things very elegant so they can later expand and make them more modular," said Miller. "We do want that, but we don't want to make people wait five years for the next product. So our focus is giving users something today and then making it more elegant underneath."

Other improvements will include enhanced visualization and data management capabilities, and to make sure that these services are available even to users with only a lower speed dial-up modem. This will enable a range of users to pose sophisticated questions, even if they don't have access to advanced computing resources.

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