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

@article{citeulike:549985, 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 (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: www.tbi.univie.ac.at/~raim/odeSolver/.}, address = {Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Univ. of Vienna, W\"{a}hringerstr. 17, 1090 Vienna, Austria.}, author = {Machn\'{e}, Rainer and Finney, Andrew and M\"{u}ller, Stefan and Lu, James and Widder, Stefanie and Flamm, Christoph }, citeulike-article-id = {549985}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {dynamic, library, modeling, ode, sbml, software, solver}, month = {March}, posted-at = {2006-09-02 11:28:31}, priority = {2}, title = {The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16527832}, year = {2006} }

TY - JOUR ID - citeulike:549985 L3 - citeulike-article-id:549985 TI - The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. JF - Bioinformatics AD - Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Univ. of Vienna, Währingerstr. 17, 1090 Vienna, Austria. SN - 1367-4803 N2 - 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: www.tbi.univie.ac.at/~raim/odeSolver/. KW - dynamic KW - library KW - modeling KW - ode KW - sbml KW - software KW - solver AU - Machné, Rainer AU - Finney, Andrew AU - Müller, Stefan AU - Lu, James AU - Widder, Stefanie AU - Flamm, Christoph PY - 2006/03/09/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16527832 ER -