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libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

Xinglai Ji·Ying Xu
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Abstract

SUMMARY: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

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AlgorithmsBiochemistryComputational BiologyComputer SimulationGene LibraryKineticsModels, GeneticProgramming LanguagesSequence Analysis, DNASoftwareStochastic ProcessesTime FactorsJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

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Xinglai Ji, Ying Xu. 2005-11-02. libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.. https://doi.org/10.1093/bioinformatics%2Fbti753

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