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Bioinformatics Advance Access published online on October 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti099
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 19, 2004
Revised September 30, 2004
Accepted October 15, 2004

Article

Evolutionary optimization with data collocation for reverse engineering of biological networks

Kuan-Yao Tsai 1 and Feng-Sheng Wang 1*

1 Department of Chemical Engineering, National Chung Cheng University, Chia-yi 621-02, Taiwan

* To whom correspondence should be addressed.
Feng-Sheng Wang, E-mail: chmfsw{at}ccu.edu.tw


  Abstract

Motivation: Modern experimental biology is moving away from analyses of single elements to whole-organism measurements. Such measured time-course data contain a wealth of information about the structure and dynamic of the pathway or network. The dynamic modeling of the whole systems is formulated as a reverse problem, which requires a well-suited mathematical model and a very efficient computational method to identify the model structure and parameters. Numerical integration for differential equations and finding global parameter values are still two major challenges in this field of the parameter estimation of nonlinear dynamic biological systems.

Results: We compare three techniques of parameter estimation for nonlinear dynamic biological systems. In the proposed scheme, the modified collocation method is applied to convert the differential equations to the system of algebraic equations. The observed time-course data are then substituted into the algebraic system equations to decouple system interactions in order to obtain the approximate model profiles. Hybrid differential evolution (HDE) with population size of five is able to find a global solution. The method is not only suited for parameter estimation, but also apply for structure identification. The solution obtained by HDE is then used as the initial starting point for a local search method to yield the refined estimates.

Availability: The algorithm, implemented by Compaq Visual Fortran Professional Edition 6.6, and the supplements are available at http://www.che.ccu.edu.tw/~bioproc/index-english.html/. IMSL Math/Library is a commercial library included in Compaq Visual Fortran Professional Edition.


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