libRoadRunner

libRoadRunner performs high-performance simulation and analysis of Systems Biology Markup Language (SBML) models for biochemical and dynamic network studies.

Key Features:

• Performance and Extensibility: Uses a custom just-in-time (JIT) compiler built on the LLVM framework to compile SBML models into native machine code for multiple processor architectures.
• Cross-Platform Compatibility: Provides runtime support on Mac OS X, Linux, Windows, and ARM-based computers such as the Raspberry Pi.
• APIs and Interfaces: Exposes C++ and C bindings and language interfaces for Python and Julia.
• Model Support: Implements the majority of the SBML specification while excluding delay and non-linear algebraic equations, and supports SBML extensions including hierarchical composition and probability distributions.
• Integration Methods and Analyses: Includes deterministic and stochastic integrators and provides steady-state analysis, sensitivity analysis, stability analysis, and structural analysis of the stoichiometric matrix.

Scientific Applications:

• Biochemical network simulation: Simulation and analysis of biochemical reaction networks encoded in SBML.
• Tissue and large-scale modeling: Simulation of tissue-scale and other large-scale models requiring efficient, repeated computation.
• Parameter estimation and sensitivity analysis: Supports extensive repeated simulations used in parameter estimation and sensitivity studies.
• Stochastic dynamics and noise analysis: Exploration of stochastic behavior and noise effects in biological processes using stochastic integrators.

Methodology:

Computational methods explicitly include LLVM-based JIT compilation of SBML into native machine code, deterministic and stochastic numerical integrators, steady-state, sensitivity and stability analyses, and structural analysis of the stoichiometric matrix, with support for SBML hierarchical composition and probability distributions and exclusion of delay and non-linear algebraic equations.