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Bioinformatics Advance Access published online on February 24, 2005
Bioinformatics, 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@oupjournals.org
Received September 15, 2004
Revised January 20, 2005
Accepted February 17, 2005

Article

Object-oriented biological system integration: a SARS coronavirus example

Daniel Shegogue 1 and W. Jim Zheng 2*

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

* To whom correspondence should be addressed.
W. Jim Zheng, E-mail: zhengw{at}musc.edu


  Abstract

Motivation: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process and 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.

Supplementary Information: Supplemental data: Table 1 and Figures 1-16.


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