Bioinformatics Advance Access originally published online on October 11, 2006
Bioinformatics 2007 23(4):480-486; doi:10.1093/bioinformatics/btl522
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Parameter estimation using Simulated Annealing for S-system models of biochemical networks
1 Department of Computer Science University of the Philippines-Diliman Munich, Germany
2 Mathematics Department University of the Philippines-Diliman Munich, Germany
3 Department Biologie I, Bereich Mikrobiologie, Ludwig-Maximilians-Universität Munich, Germany
4 Medizinische Fakultät, Physiologisches Institut, Ludwig-Maximilians-Universität Munich, Germany
5 Physics Department & Center for NanoScience Ludwig-Maximilians-University Munich, Germany
*To whom correspondence should be addressed.
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Abstract |
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Motivation: High-throughput technologies now allow the acquisition of biological data, such as comprehensive biochemical time-courses at unprecedented rates. These temporal profiles carry topological and kinetic information regarding the biochemical network from which they were drawn. Retrieving this information will require systematic application of both experimental and computational methods.
Results: S-systems are non-linear mathematical approximative models based on the power-law formalism. They provide a general framework for the simulation of integrated biological systems exhibiting complex dynamics, such as genetic circuits, signal transduction and metabolic networks. We describe how the heuristic optimization technique simulated annealing (SA) can be effectively used for estimating the parameters of S-systems from time-course biochemical data. We demonstrate our methods using three artificial networks designed to simulate different network topologies and behavior. We then end with an application to a real biochemical network by creating a working model for the cadBA system in Escherichia coli.
Availability: The source code written in C++ is available at http://www.engg.upd.edu.ph/~naval/bioinformcode.html. All the necessary programs including the required compiler are described in a document archived with the source code.
Contact: gonzalez{at}bio.ifi.lmu.de
Supplementary information: Supplementary material is available at Bioinformatics online.
Associate Editor: Martin Bishop
Received on July 6, 2006; revised on September 13, 2006; accepted on September 21, 2006
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