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Bioinformatics Advance Access originally published online on February 24, 2005
Bioinformatics 2005 21(10):2502-2509; doi:10.1093/bioinformatics/bti344
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Object-oriented biological system integration: a SARS coronavirus example

Daniel Shegogue 1 and W. Jim Zheng 1,2,*

1Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina 135 Cannon Street, PO Box 250835, Charleston, SC 29425, USA
2Bioinformatics Core Facility, Hollings Cancer Center, Medical University of South Carolina 135 Cannon Street, PO Box 250835, Charleston, SC 29425, USA

*To whom correspondence should be addressed.

Motivation: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary.

Results: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems.

Availability: A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm

Contact: zhengw{at}musc.edu

Supplementary information: Supplemental data: Table 1 and Figures 1–16.


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