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