SOSlib

The SMBL ODE Solver Library

SOSlib (Machné et al., 2006) 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). 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.

References

2006

  1. The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
    Rainer Machné, Andrew Finney, Stefan Müller, and 3 more authors
    Bioinformatics, 2006
    DOI