libRoadRunner: A High Performance SBML Simulation and Analysis Library

Autor: James A. Glazier, Matthias König, M. Swat, Endre Somogyi, Herbert M. Sauro, J. Kyle Medley, Jean-Marie C. Bouteiller
Rok vydání: 2015
Předmět:
Statistics and Probability
FOS: Computer and information sciences
Quantitative Biology - Subcellular Processes
Computer science
computer.software_genre
Models
Biological
Biochemistry
03 medical and health sciences
0302 clinical medicine
Software
Cell Adhesion
Humans
Computer Simulation
SBML
MATLAB
Molecular Biology
Subcellular Processes (q-bio.SC)
030304 developmental biology
computer.programming_language
Neurons
0303 health sciences
Application programming interface
business.industry
Programming language
Systems Biology
Models
Theoretical
Python (programming language)
Original Papers
Computer Science Applications
Computational Mathematics
Liver
Computational Theory and Mathematics
Just-in-time compilation
FOS: Biological sciences
Operating system
Programming Languages
Computer Science - Mathematical Software
Compiler
business
computer
Machine code
Mathematical Software (cs.MS)
030217 neurology & neurosurgery
DOI: 10.48550/arxiv.1503.01095
Popis: Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. 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 interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB (www.mathworks.com) and SciPy (http://www.scipy.org/), making it fast and easy to learn. 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 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 non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. Availability and implementation: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. Contacts: hsauro@u.washington.edu or somogyie@indiana.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Databáze: OpenAIRE
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