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Bioinformatics Advance Access published online on November 2, 2005
Bioinformatics, 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
Received June 28, 2005
Revised September 6, 2005
Accepted October 27, 2005

Applications note

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

Xinglai Ji 1 and Ying Xu 2*

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

* To whom correspondence should be addressed.
Ying Xu, E-mail: xyn{at}bmb.uga.edu


  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 nonlinear 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, a 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/.

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


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