pCMALib: a parallel fortran 90 library for the evolution strategy with covariance matrix adaptation
Proceedings of the 11th Annual conference on Genetic and evolutionary computation
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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 (μ, λ)-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/ Contact: xyn@bmb.uga.edu Supplementary information: Detailed documentation for libSRES is available at http://csbl.bmb.uga.edu/~jix/science/libSRES/