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Bioinformatics Advance Access originally published online on March 9, 2006
Bioinformatics 2006 22(11):1406-1407; doi:10.1093/bioinformatics/btl086
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks

Rainer Machné 1, Andrew Finney 2, Stefan Müller 3, James Lu 3, Stefanie Widder 1 and Christoph Flamm 1,4,*

1 Institute for Theoretical Chemistry, University of Vienna 1090 Vienna, Austria
2 Physiomics PLC, Magdalen Centre Oxford Science Park, Oxford, OX4 4GA, UK
3 Johann Radon Institute for Computational and Applied Mathematics (RICAM), Austrian Academy of Sciences 4040 Linz, Austria
4 Bioinformatics, Institute for Computer Science, University of Leipzig 04107 Leipzig, Germany

*To whom correspondence should be addressed.

The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of ordinary differential equations, their Jacobian matrix and other derivatives. SUNDIALS' CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a rough overview on the behavior of different tools and are discussed in the Supplementary Material. The native application program interface provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBML and non SBML data sources. Optional modules based on XMGrace and Graphviz allow quick inspection of structure and dynamics.

Availability: www.tbi.univie.ac.at/~raim/odeSolver/

Contact: xtof{at}tbi.univie.ac.at

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on January 11, 2006; revised on February 15, 2006; accepted on March 4, 2006

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