ArticleBioinformatics (Oxford, England)2023
libRoadRunner 2.0: a high performance SBML simulation and analysis library.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- A digital twin of glimepiride for personalized and stratified diabetes treatment.Frontiers in pharmacology · 2025Article
- Kinetic principles of chemical cross-link formation for protein-protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Curating models from BioModels: Developing a workflow for creating OMEX files.bioRxiv : the preprint server for biology · 2024Article
- Generating synthetic signaling networks for in silico modeling studies.Journal of theoretical biology · 2024Article
- A next-generation dynamic programming language Julia: Its features and applications in biological science.Journal of advanced research · 2024Review
- Mathematical Modeling and Inference of Epidermal Growth Factor-Induced Mitogen-Activated Protein Kinase Cell Signaling Pathways.International journal of molecular sciences · 2024Review
- Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems.Bioinformatics (Oxford, England) · 2024Article
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Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationThis article presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using the systems biology markup language (SBML).
resultslibRoadRunner is a self-contained library, able to run either as a component inside other tools via its C++, C and Python APIs, or 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 fast enough to simulate extremely large models or repeated runs in reasonable timeframes. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) as well as several SBML extensions such as hierarchical composition and probability distributions. It offers multiple deterministic and stochastic integrators, as well as tools for steady-state, sensitivity, stability and structural analyses. AVAILABILITY AND IMPLEMENTATION: libRoadRunner binary distributions for Windows, Mac OS and Linux, Julia and Python bindings, source code and documentation are all available at https://github.com/sys-bio/roadrunner, and Python bindings are also available via pip. The source code can be compiled for the supported systems as well as in principle any system supported by LLVM-13, such as ARM-based computers like the Raspberry Pi. The library is licensed under the Apache License Version 2.0.
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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.