Nonuniform sampling for global optimization of kinetic rate constants in biological pathways
Proceedings of the 38th conference on Winter simulation
Inferring Gene Regulatory Networks using Differential Evolution with Local Search Heuristics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Parameter estimation in modulated, unbranched reaction chains within biochemical systems
Computational Biology and Chemistry
Inference of genetic networks using linear programming machines: application of a priori knowledge
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
A parameter estimation approach for non-linear systems biology models using spline approximation
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Genetic Networks and Soft Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Parameter Estimation Using Metaheuristics in Systems Biology: A Comprehensive Review
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multi-stage evolutionary algorithms for efficient identification of gene regulatory networks
EuroGP'06 Proceedings of the 2006 international conference on Applications of Evolutionary Computing
Reconstructing metabolic networks using interval analysis
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Inference of Biological S-System Using the Separable Estimation Method and the Genetic Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SEAL'12 Proceedings of the 9th international conference on Simulated Evolution and Learning
An Optimization Rule for In Silico Identification of Targeted Overproduction in Metabolic Pathways
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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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 that 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 can be applied for structure identification. The solution obtained by HDE is then used as the 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. Contact: chmfsw@ccu.edu.tw