Libroadrunner

Last updated
libroadrunner
Initial releaseMarch 23, 2015;9 years ago (2015-03-23)
Stable release
2.6.0 / March 26, 2024;28 days ago (2024-03-26)
Written in Python, C++, C, FORTRAN
Operating system Linux, macOS and Microsoft Windows
License Apache License
Website github.com/sys-bio/roadrunner

libRoadRunner is a C/C++ software library that supports simulation of SBML based models.. [1] It uses LLVM to generate extremely high-performance code and is the fastest SBML-based simulator currently available. [2] Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of Python bindings that allow it to be easily used from Python as well as a set of bindings for Julia. [3]

Contents

libroadrunner is often paired with Tellurium, [4] which adds additional functionality such as Antimony [5] scripting.

Capabilities

Applications

libroadrunner has been widely used in the systems biology community for doing research in systems biology modeling, as well as being a host for other simulation platforms.

Software applications that use libroadrunner

Research applications

libroadrunner has been used in a large variety of research projects. The following lists a small number of those studies:

Notability

A number of reviews and commentaries have been written that discuss libroadrunner:

Development

Development of libroadrunner is primarily funded through research grants from the National Institutes of Health [29]

See also

Related Research Articles

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<span class="mw-page-title-main">Systems Biology Ontology</span>

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<span class="mw-page-title-main">Minimum information about a simulation experiment</span>

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<span class="mw-page-title-main">JSBML</span>

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References

  1. ↑ Somogyi, Endre T.; Bouteiller, Jean-Marie; Glazier, James A.; König, Matthias; Medley, J. Kyle; Swat, Maciej H.; Sauro, Herbert M. (15 October 2015). "libRoadRunner: a high performance SBML simulation and analysis library: Table 1". Bioinformatics. 31 (20): 3315–3321. doi:10.1093/bioinformatics/btv363. PMC   4607739 . PMID   26085503.
  2. ↑ Maggioli, F; Mancini, T; Tronci, E (1 April 2020). "SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems". Bioinformatics. 36 (7): 2165–2172. arXiv: 2106.02609 . doi:10.1093/bioinformatics/btz860. PMID   31738386.
  3. ↑ Welsh, Ciaran; Xu, Jin; Smith, Lucian; König, Matthias; Choi, Kiri; Sauro, Herbert M (1 January 2023). "libRoadRunner 2.0: a high performance SBML simulation and analysis library". Bioinformatics. 39 (1). arXiv: 1503.01095 . doi:10.1093/bioinformatics/btac770. PMID   36478036.
  4. ↑ Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018). "Tellurium: An extensible python-based modeling environment for systems and synthetic biology". Biosystems. 171: 74–79. Bibcode:2018BiSys.171...74C. doi:10.1016/j.biosystems.2018.07.006. PMC   6108935 . PMID   30053414.
  5. ↑ Smith, L. P.; Bergmann, F. T.; Chandran, D.; Sauro, H. M. (15 September 2009). "Antimony: a modular model definition language". Bioinformatics. 25 (18): 2452–2454. doi:10.1093/bioinformatics/btp401. PMC   2735663 . PMID   19578039.
  6. ↑ Hindmarsh, Alan C.; Brown, Peter N.; Grant, Keith E.; Lee, Steven L.; Serban, Radu; Shumaker, Dan E.; Woodward, Carol S. (September 2005). "SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers". ACM Transactions on Mathematical Software. 31 (3): 363–396. doi:10.1145/1089014.1089020. OSTI   15002968. S2CID   6826941.
  7. ↑ Deuflhard, P (2004). Newton Methods for Nonlinear Problems. Springer-Verlag, NY.
  8. ↑ Hofmeyr, Jannie (2001). "Metabolic control analysis in a nutshell". Proceedings of the 2nd International Conference on Systems Biology. S2CID   17007756.
  9. ↑ Yip, Evan; Sauro, Herbert (2021). "Computing Sensitivities in Reaction Networks using Finite Difference Methods". arXiv: 2110.04335 .{{cite journal}}: Cite journal requires |journal= (help)
  10. ↑ Kerkhoven, Eduard J.; Achcar, Fiona; Alibu, Vincent P.; Burchmore, Richard J.; Gilbert, Ian H.; Trybiło, Maciej; Driessen, Nicole N.; Gilbert, David; Breitling, Rainer; Bakker, Barbara M.; Barrett, Michael P. (5 December 2013). "Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei". PLOS Computational Biology. 9 (12): e1003371. Bibcode:2013PLSCB...9E3371K. doi: 10.1371/journal.pcbi.1003371 . PMC   3854711 . PMID   24339766.
  11. ↑ Reyes, Brandon C; Otero-Muras, Irene; Shuen, Michael T; Tartakovsky, Alexandre M; Petyuk, Vladislav A (1 June 2020). "CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks". Bioinformatics. 36 (12): 3922–3924. doi: 10.1093/bioinformatics/btaa241 . PMID   32289149.
  12. ↑ Nguyen, Lan K.; Degasperi, Andrea; Cotter, Philip; Kholodenko, Boris N. (December 2015). "DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks". Scientific Reports. 5 (1): 12569. Bibcode:2015NatSR...512569N. doi:10.1038/srep12569. PMC   4518224 . PMID   26220783.
  13. ↑ Haiman, Zachary B.; Zielinski, Daniel C.; Koike, Yuko; Yurkovich, James T.; Palsson, Bernhard O. (28 January 2021). "MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics". PLOS Computational Biology. 17 (1): e1008208. Bibcode:2021PLSCB..17E8208H. doi: 10.1371/journal.pcbi.1008208 . PMC   7872247 . PMID   33507922.
  14. ↑ Neumann, Jacob; Lin, Yen Ting; Mallela, Abhishek; Miller, Ely F; Colvin, Joshua; Duprat, Abell T; Chen, Ye; Hlavacek, William S; Posner, Richard G (4 March 2022). "Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit". Bioinformatics. 38 (6): 1770–1772. doi:10.1093/bioinformatics/btac004. PMC   10060707 . PMID   34986226.
  15. ↑ Ghaffarizadeh, Ahmadreza; Heiland, Randy; Friedman, Samuel H.; Mumenthaler, Shannon M.; Macklin, Paul (23 February 2018). "PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems". PLOS Computational Biology. 14 (2): e1005991. Bibcode:2018PLSCB..14E5991G. doi: 10.1371/journal.pcbi.1005991 . PMC   5841829 . PMID   29474446.
  16. ↑ Ortega, Oscar O.; Lopez, Carlos F. (January 2020). "Interactive Multiresolution Visualization of Cellular Network Processes". iScience. 23 (1): 100748. Bibcode:2020iSci...23j0748O. doi:10.1016/j.isci.2019.100748. PMC   6941861 . PMID   31884165.
  17. ↑ Shaikh, Bilal; Marupilla, Gnaneswara; Wilson, Mike; Blinov, Michael L; Moraru, Ion; Karr, Jonathan R (2 July 2021). "RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats". Nucleic Acids Research. 49 (W1): W597–W602. doi:10.1093/nar/gkab411. PMC   8262693 . PMID   34019658.
  18. ↑ Konig, Matthias. "SBMLSim". GitHub .
  19. ↑ Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018). "Tellurium: An extensible python-based modeling environment for systems and synthetic biology". Biosystems. 171: 74–79. Bibcode:2018BiSys.171...74C. doi:10.1016/j.biosystems.2018.07.006. PMC   6108935 . PMID   30053414.
  20. ↑ Sego, T.J.; Sluka, James P.; Sauro, Herbert M.; Glazier, James A. (29 November 2022). "Tissue Forge: Interactive Biological and Biophysics Simulation Environment". doi:10.1101/2022.11.28.518300.{{cite journal}}: Cite journal requires |journal= (help)
  21. ↑ Tickman, Benjamin I.; Burbano, Diego Alba; Chavali, Venkata P.; Kiattisewee, Cholpisit; Fontana, Jason; Khakimzhan, Aset; Noireaux, Vincent; Zalatan, Jesse G.; Carothers, James M. (March 2022). "Multi-layer CRISPRa/i circuits for dynamic genetic programs in cell-free and bacterial systems". Cell Systems. 13 (3): 215–229.e8. doi: 10.1016/j.cels.2021.10.008 . PMID   34800362. S2CID   244430298.
  22. ↑ Salazar-Cavazos, Emanuel; Nitta, Carolina Franco; Mitra, Eshan D.; Wilson, Bridget S.; Lidke, Keith A.; Hlavacek, William S.; Lidke, Diane S. (19 March 2020). "Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes". Molecular Biology of the Cell. 31 (7): 695–708. doi:10.1091/mbc.E19-09-0548. PMC   7202077 . PMID   31913761. S2CID   210119415.
  23. ↑ Douilhet, Gemma; Niranjan, Mahesan; Vallejo, Andres; Clayton, Kalum; Davies, James; Sirvent, Sofia; Pople, Jenny; Ardern-Jones, Michael R; Polak, Marta E (23 February 2022). "Genetic Algorithm with Rank Selection optimises robust parameter estimation for systems biology models". bioRxiv   10.1101/2022.02.22.481394 .
  24. ↑ Schmiester, Leonard; Weindl, Daniel; Hasenauer, Jan (7 December 2021). "Efficient gradient-based parameter estimation for dynamic models using qualitative data". Bioinformatics. 37 (23): 4493–4500. doi:10.1093/bioinformatics/btab512. PMC   8652033 . PMID   34260697.
  25. ↑ Yang, Yongliang; Filipovic, David; Bhattacharya, Sudin (April 2022). "A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver". Hepatology Communications. 6 (4): 750–764. doi:10.1002/hep4.1848. PMC   8948569 . PMID   34726355. S2CID   240422386.
  26. ↑ "Bifurcation Analysis".
  27. ↑ Maggioli, F; Mancini, T; Tronci, E (1 April 2020). "SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems". Bioinformatics. 36 (7): 2165–2172. arXiv: 2106.02609 . doi:10.1093/bioinformatics/btz860. PMID   31738386.
  28. ↑ Köster, Till; Warnke, Tom; Uhrmacher, Adelinde M. (30 April 2022). "Generating Fast Specialized Simulators for Stochastic Reaction Networks via Partial Evaluation". ACM Transactions on Modeling and Computer Simulation. 32 (2): 1–25. doi:10.1145/3485465. S2CID   247273613.
  29. ↑ Sauro, Herbert. "Development Support".
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