SOSlib (SBML ODE Solver Library): SOSlib is both a programming library and a command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). It is written in ANSI/ISO C and distributed under the terms of the GNU Lesser General Public License (LGPL). The package employs libSBML’s AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems. The native API provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of powerful and efficient analytic applications, hybrid solvers or multi-scale models with interfaces to non SBML data sources. Optional modules based on Graphviz and XMGrace allow a quick inspection of a model’s structure and dynamics. All functionalities are accessible directly via a command-line application and several example programs.

References in zbMATH (referenced in 4 articles )

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  1. Sanguinetti, Guido (ed.); Huynh-Thu, Vân Anh (ed.): Gene regulatory networks. Methods and protocols (2019)
  2. Lu, James; August, Elias; Koeppl, Heinz: Inverse problems from biomedicine: inference of putative disease mechanisms and robust therapeutic strategies (2013)
  3. Rybiński, Mikołaj; Gambin, Anna: Model-based selection of the robust JAK-STAT activation mechanism (2012)
  4. Machné, Rainer; Finney, Andrew; Müller, Stefan; Lu, James; Widder, Stefanie; Flamm, Christoph: The sbml ODE solver library: A native api for symbolic and fast numerical analysis of reaction networks (2006) ioport