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Bioinformatics Advance Access originally published online on November 2, 2005
Bioinformatics 2006 22(1):124-126; doi:10.1093/bioinformatics/bti753
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Xinglai Ji 1 and Ying Xu 2,*

1Computational Biology Institute, Oak Ridge National Laboratory Oak Ridge, TN 37831, USA
2Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia Athens, GA 30602-7229, USA

*To whom correspondence should be addressed.

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, {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/

Contact: xyn{at}bmb.uga.edu

Supplementary information: Detailed documentation for libSRES is available at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Received on June 28, 2005; revised on September 6, 2005; accepted on October 27, 2005

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