TBI-Preprint 05-03-002
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Titel:
The SBML ODE Solver Library: a native API for symbolic and
fast numerical analysis of reaction networks.
Author(s):
Rainer Machne,
Andrew Finney,
Stefan Müller,
James Lu,
Stefanie Widder,
Christoph Flamm
Appeared in:
Bioinformatics 2006
Abstract:
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 (ODE
s), 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
Alternative Numbers:
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Last modified: 2006-05-11 12:22:37 xtof