Recently patented Biology Workbench reveals itself as excellent informatics management tool

Urbana 09 February 1999 In medicine as well as in biology, there exists an urgent need for global communication of information. The efficient exchange of data might reduce the time-consuming administrative burden, faced by physicians, and facilitate the computations for gene sequencing for biology researchers. The Web-based Biology Workbench enables scientists and medical professionals to spend more time on respective research and patient care. This powerful management tool has been developed by the team of Shankar Subramaniam, a senior researcher from the National Computational Science Alliance (NCSA) at the University of Illinois.

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In medicine as well as in biology, there exists an urgent need for global communication of information. The efficient exchange of data might reduce the time-consuming administrative burden, faced by physicians, and facilitate the computations for gene sequencing for biology researchers. The Web-based Biology Workbench enables scientists and medical professionals to spend more time on respective research and patient care. This powerful management tool has been developed by the team of Shankar Subramaniam, a senior researcher from the National Computational Science Alliance (NCSA) at the University of Illinois.

The Biology Workbench has been granted a United States patent as an innovative system and method for managing informatics in a speciality field. Initially, the tool has been designed to use the World Wide Web for the access, analysis, and performance of computations on a number of biological sequences and structure databases. However, the patent extends beyond the field of biology research to implement the inter-operable Web interface also for other scientific disciplines, using large data sets, such as medicine. All that is required to fully benefit from the toolkit is a personal workstation and a network connection.

The medical community has several disparate information systems in use, some of which are computer-based and many of which are based on paper records. The paper record systems often date from early in this century. In turn, the computer-based systems are frequently applied for very specific or narrow-scope applications. The current information systems include various methodologies, like CD-ROMs, commercial on line systems of limited scope and functionality, and hundreds of individual Web-based pages. Throughout the years, data repositories have been developed and maintained to contain case histories, pharmaceutical information, and other records.

The most obvious area for use of data repositories are the fields of molecular and structural biology research. Over the years, genome sequencing projects have been set up for a variety of organisms, of which the human genome is calling most to our imagination. Sequence data has grown incredibly fast. As sequencing and structure determination projects proceeded, the nature of bench work in both fields of molecular and structural biology have radically changed and become increasingly dependent upon information retrieval. The present workbench offers an information management tool, providing users in a specialized field with a gateway for global access and use of the various remote data repositories and services which are related to their specific field.

A local workstation with a browser application is connected to a server over a network with access to a plurality of remote data repositories. The server is running a gateway programme, which allows to receive a query request in a first format from the user over the network. A query translator routine has to translate the query request from the first format to a plurality of different formats. Subsequently, the translated query requests are sent to the remote data repositories and results are received therefrom. The gateway programme also includes a results translator routine for translation of the results which are obtained from the remote data repositories into results in the first format to send back in the first format to the user's workstation.

In a further aspect of the system, query results can be used as input data to analysis tools and programmes since the gateway programme equally offers a translator routine, translating the query results into input data for remote tools or analysis programmes. A driver routine launches the remote analysis programme. Afterwards, the computed results are being translated from the remote analysis programme into results in the first format, in order to send the results in the first format to the user's workstation. In this embodiment, the network is the Internet and the first format is HTML.

Information management systems, similar to the ones for biologists and the medical community, may be tailored for other fields or specialities. In fact, the National Computational Science Alliance is already preparing toolkits for a Chemical Engineering Workbench as well as an Environmental Hydrology Workbench. Each of these workbenches will offer scientists access to a wide range of computational tools in their disciplines by means of a simple Web interface. Please, visit the Web site of the US Patent and Trademark Office for further information on the patent for the Biology workbench.


Leslie Versweyveld

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