ArticleBioinformatics (Oxford, England)2015
libRoadRunner: a high performance SBML simulation and analysis library.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Article
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- A digital twin of glimepiride for personalized and stratified diabetes treatment.Frontiers in pharmacology · 2025Article
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- Generating synthetic signaling networks for in silico modeling studies.Journal of theoretical biology · 2024Article
- TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level.International journal of molecular sciences · 2024Article
- Kiphynet: an online network simulation tool connecting cellular kinetics and physiological transport.Metabolomics : Official journal of the Metabolomic Society · 2024Article
- Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.Journal of integrative bioinformatics · 2024Article
- Rational strain design with minimal phenotype perturbation.Nature communications · 2024Article
- SimService: a lightweight library for building simulation services in Python.Bioinformatics (Oxford, England) · 2024Article
- Article
- PhysiCell Studio: a graphical tool to make agent-based modeling more accessible.GigaByte (Hong Kong, China) · 2024Article
- Tissue Forge: Interactive biological and biophysics simulation environment.PLoS computational biology · 2023Article
- BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells.NPJ systems biology and applications · 2023Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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Abstract
motivationThis 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.
resultslibRoadRunner 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 ( WWWMATHWORKSCOM: ) and SciPy ( HTTP//WWWSCIPYORG/: ), 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.