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

摘要: 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 written ISO C distributed under open source LGPL license. package employs libSBML structures formula representation associated functions to construct system ordinary differential equations, their Jacobian matrix other derivatives. SUNDIALS' CVODES incorporated integration sensitivity analysis. Preliminary benchmarking results give rough overview on behavior different tools are discussed Supplementary Material. native application program interface provides fine-grained interfaces all internal data structures, operations routines, enabling construction very efficient analytic applications hybrid or multi-scale solvers with non sources. Optional modules based XMGrace Graphviz allow quick inspection structure dynamics. Availability: www.tbi.univie.ac.at/~raim/odeSolver/ Contact: xtof@tbi.univie.ac.at Supplementary information: available at Bioinformatics online.