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Open Access Highly Accessed Methodology article

Systems biology driven software design for the research enterprise

John Boyle*, Christopher Cavnor, Sarah Killcoyne and Ilya Shmulevich

Author Affiliations

Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA

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BMC Bioinformatics 2008, 9:295  doi:10.1186/1471-2105-9-295

Published: 25 June 2008

Abstract

Background

In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools.

Results

We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model.

Conclusion

By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.