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libRoadRunner: a high performance SBML simulation and analysis library.

Endre T Somogyi1, Jean-Marie Bouteiller2, James A Glazier1

  • 1Biocomplexity Institute and Department of Physics, Indiana University, Bloomington, IN, 47405, USA.

Bioinformatics (Oxford, England)
|June 19, 2015
PubMed
Summary
This summary is machine-generated.

libRoadRunner is an open-source software library for simulating Systems Biology Markup Language (SBML) models. It offers high performance for large-scale problems and interactive analysis, supporting various SBML features and providing multiple simulation tools.

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Area of Science:

  • Systems biology
  • Computational biology
  • Biochemical network modeling

Background:

  • Systems Biology Markup Language (SBML) is the standard for dynamic biochemical networks.
  • Efficient simulation tools are crucial for large-scale and interactive analyses.
  • libRoadRunner addresses the need for a high-performance, cross-platform solution.

Purpose of the Study:

  • To present libRoadRunner, an extensible, open-source software library.
  • To enable high-performance simulation and analysis of SBML models.
  • To support large-scale, repeated, and interactive simulation studies.

Main Methods:

  • Developed as a self-contained library with C++ and C bindings.
  • Features a Python API for ease of use, similar to MATLAB and SciPy.
  • Utilizes a custom Just-In-Time (JIT) compiler based on LLVM to compile SBML models to native machine code.
  • Supports a broad range of SBML specifications, including extensions, and offers various deterministic and stochastic integrators.

Main Results:

  • libRoadRunner achieves high performance suitable for tissue models and extensive simulations.
  • The library is cross-platform (Mac OS X, Linux, Windows, ARM-based) and open-source (Apache License 2.0).
  • Provides tools for steady-state, stability, and structural analysis of stoichiometric matrices.
  • Supports interactive simulations and integration into other software tools.

Conclusions:

  • libRoadRunner is a versatile and efficient tool for systems biology research.
  • Its performance and flexibility facilitate complex model simulations and analyses.
  • The library is readily available with comprehensive online documentation and support.