libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library

TL;DR

libRoadRunner 2.0 is a high-performance, cross-platform library for SBML model simulation and analysis, utilizing JIT compilation for fast execution and supporting extensive SBML features and extensions.

Contribution

It introduces a new version of libRoadRunner with JIT compilation, broad SBML support, and multi-language interfaces, enhancing performance and flexibility for systems biology modeling.

Findings

Supports large models with native machine code execution

Provides multiple deterministic and stochastic integrators

Enables comprehensive analysis including steady-state and sensitivity

Abstract

Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python or Julia interface. libRoadRunner uses a custom Just-In-Time JIT compiler built on the widely-used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a large variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and nonlinear algebraic equations) and including several SBML extensions such as composition and distributions. It offers multiple deterministic and stochastic integrators, as well as tools for steady-state, sensitivity, stability analysis, and structural analysis of the stoichiometric matrix. Availability: libRoadRunner binary distributions are available for Mac OS X, Linux, and Windows. The library is licensed under the Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi and can in principle be compiled on any system supported by LLVM-13. http://sys-bio.github.io/roadrunner/index.html provides online documentation, full build instructions, binaries, and a git source repository.