TBI-Preprint 05-03-002

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Titel:
SBML ODE Solver Library: a command-line tool and library for numerical analysis of reaction networks

Author(s):
Rainer Machne, Andrew Finney, Stefanie Widder, Stefan Müller, Christoph Flamm

Submitted to:
Bioinformatics 2005

Abstract:
The SBML ODE Solver Library (SOSlib) is a command-line oriented tool and programming library for construction and numerical integration of a system of ordinary differential equations (ODE) from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ANSI C, provides bindings for a variety of scripting languages and is distributed under LGPL license. The package uses the SBML library libSBML for parsing SBML models and construction of ODE systems, and CVODE for numerical integration. Optional data visualization modules based on XMGrace and Graphviz allow a quick inspection of the model's structure and dynamics, providing a transparent and direct interface to SBML models, which is especially useful for educational purposes.

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

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Last modified: 2005-09-14 16:36:15 xtof