The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.
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.
Machné
Rainer
R
Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria.
Finney
Andrew
A
Müller
Stefan
S
Lu
James
J
Widder
Stefanie
S
Flamm
Christoph
C
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D015723:Gene Library; D008954:Models, Biological; D008962:Models, Theoretical; D011381:Programming Languages; D012985:Software Design; D049490:Systems Biology