Titel
The SBML ODE Solver Library: A native API for symbolic and fast numerical analysis of reaction networks
Autor*in
Andrew Finney
Physiomics PLC, The Magdalen Centre
Autor*in
Stefan Müller
Johann Radon Institute for Computational and Applied Mathematics (RICAM)
... show all
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, 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. Π2006 Oxford University Press.
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:245111
Erschienen in
Titel
Bioinformatics
Band
22
Ausgabe
11
Seitenanfang
1406
Seitenende
1407
Erscheinungsdatum
01.12.2006
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