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

TheSBMLODESolver Library (SOSlib) is a programming library for sym-bolicandnumericalanalysisofchemical reactionnetworkmodelsencoded in theSystemsBiologyMarkupLanguage(SBML). It iswritten in ISOCand distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a systemof ordinary differential equations, their Jacobianmatrix and other derivatives. SUNDIALS ’ CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a roughoverviewon thebehavior of different tools andarediscussed in the Supplementary Material. The native application program interface pro-vides fine-grained interfaces toall internal datastructures, symbolicopera-tions and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBMLandnonSBMLdatasources.OptionalmodulesbasedonXMGrace and Graphviz allow quick inspection of structure and dynamics