• libRoadRunner 2.0: a high perf...

Treffer: libRoadRunner 2.0: a high performance SBML simulation and analysis library.

Title:
libRoadRunner 2.0: a high performance SBML simulation and analysis library.
Authors:
Welsh C; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA., Xu J; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA., Smith L; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA., König M; Institute of Biology, Institute of Theoretical Biology, Humboldt-University Berlin, Berlin 10115, Germany., Choi K; School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea., Sauro HM; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2023 Jan 01; Vol. 39 (1).
Publication Type:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Programming Languages* , Systems Biology*, Models, Biological ; Computer Simulation ; Software ; Language
References:
Bioinformatics. 2020 Apr 1;36(7):2165-2172. (PMID: 31738386)
Nucleic Acids Res. 2020 Jan 8;48(D1):D407-D415. (PMID: 31701150)
Front Bioeng Biotechnol. 2021 Apr 29;9:657244. (PMID: 33996781)
J Integr Bioinform. 2019 Jun 20;16(2):. (PMID: 31219795)
BMC Bioinformatics. 2022 Jan 4;23(1):1. (PMID: 34983366)
Bioinformatics. 2009 Sep 15;25(18):2452-4. (PMID: 19578039)
Nucleic Acids Res. 2021 Jul 2;49(W1):W597-W602. (PMID: 34019658)
Methods Cell Biol. 2012;110:325-66. (PMID: 22482955)
PLoS Comput Biol. 2021 Jan 28;17(1):e1008208. (PMID: 33507922)
Front Physiol. 2021 Nov 22;12:757293. (PMID: 34880776)
J Integr Bioinform. 2020 Jul 20;17(2-3):. (PMID: 32750035)
IET Syst Biol. 2008 Sep;2(5):352-62. (PMID: 19045830)
Front Physiol. 2021 Nov 22;12:730418. (PMID: 34880771)
iScience. 2020 Jan 24;23(1):100748. (PMID: 31884165)
Bioinformatics. 2005 Feb 15;21(4):560-1. (PMID: 15454409)
Bioinformatics. 2013 Jun 1;29(11):1474-6. (PMID: 23564843)
Sci Rep. 2015 Jul 29;5:12569. (PMID: 26220783)
Mol Syst Biol. 2020 Aug;16(8):e9110. (PMID: 32845085)
Mol Syst Biol. 2013;9:646. (PMID: 23423320)
Bioinformatics. 2009 Nov 1;25(21):2848-9. (PMID: 19628507)
Bioinformatics. 2006 Dec 15;22(24):3067-74. (PMID: 17032683)
Bioinformatics. 2015 Oct 15;31(20):3315-21. (PMID: 26085503)
PLoS Comput Biol. 2011 Oct;7(10):e1002155. (PMID: 21998560)
Bioinformatics. 2021 Sep 23;:. (PMID: 34554191)
Biosystems. 2018 Sep;171:74-79. (PMID: 30053414)
PLoS Comput Biol. 2018 Feb 23;14(2):e1005991. (PMID: 29474446)
Bioinformatics. 2022 Jan 05;:. (PMID: 34986226)
Bioinformatics. 2003 Mar 1;19(4):524-31. (PMID: 12611808)
Grant Information:
R01 GM123032 United States GM NIGMS NIH HHS; 1933453 National Science Foundation
Entry Date(s):
Date Created: 20221208 Date Completed: 20230110 Latest Revision: 20230322
Update Code:
20250114
PubMed Central ID:
PMC9825722
DOI:
10.1093/bioinformatics/btac770
PMID:
36478036
Database:
MEDLINE

Weitere Informationen

Motivation: This 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).
Results: libRoadRunner 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.
(© The Author(s) 2022. Published by Oxford University Press.)