TBI-Preprint 05-03-002

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

Rainer Machne, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm

Appeared in:
Bioinformatics 2006

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 (ODEs), 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 API 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: Source Code

Keywords: reaction networks, ordinary differential equations, ODE, numerical integration, data visualization, systems biology markup language, SBML

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Last modified: 2006-05-11 12:22:37 xtof