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README.md

SBML Solver

Copyright 2018

SBML Solver is high performance and portable simulation engine for systems and synthetic biology, which is a continuation of the original libRoadRunner project.

SBML Solver 1.0 supports the following features

  • Time Dependent Simulation (with optional conservation law reduction) using CVODE
  • Supports SBML Level 2 to 3 but currently excludes algebraic rules and delay differential equations
  • Uses latest libSBML distribution
  • Defaults to LLVM code generation on the backend, resulting is very fast simulation times
  • Optional generation of model C code and linking at run-time
  • Add plugins, distribution comes with Levenberg-Marquardt optimizer plugin
  • Compute steady state
  • Metabolic Control Analysis
  • Frequency Domain Analysis
  • Access to:
    • Eigenvalues and Eigenvectors
    • Jacobian, full and reduced
    • Structural Matrices of the stoichiometry matrix

Availability

SBML Solver is licensed for free as an open source programmatic library for use in other applications and as a standalone command line driven application. Its C++ API, C API, and Python APIs have comprehensive documentation. On Windows, OS X, and Linux binary files can be

downloaded from https://github.com/AndySomogyi/sbmlsolver ready for use.

Acknowledgements

This work is funded by NIGMS grant: GM081070

Licence

Licensed under the GNU Library General Public License (LGPL), Version 2.0 (the License); you may not use this file except in compliance with the License. You may obtain a copy of the License at

YOU CANNOT: redistribute any piece of this software without proper attribution;