Libroadrunner

Last updated
libroadrunner
Initial releaseMarch 23, 2015;9 years ago (2015-03-23)
Stable release
2.6.0 / March 26, 2024;8 months 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 [30]

See also

Related Research Articles

<span class="mw-page-title-main">Computational biology</span> Branch of biology

Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer science and engineering which uses bioengineering to build computers.

The Blue Brain Project is a Swiss brain research initiative that aims to create a digital reconstruction of the mouse brain. The project was founded in May 2005 by the Brain Mind Institute of École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. Its mission is to use biologically-detailed digital reconstructions and simulations of the mammalian brain to identify the fundamental principles of brain structure and function.

The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today.

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

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling.

Systems immunology is a research field under systems biology that uses mathematical approaches and computational methods to examine the interactions within cellular and molecular networks of the immune system. The immune system has been thoroughly analyzed as regards to its components and function by using a "reductionist" approach, but its overall function can't be easily predicted by studying the characteristics of its isolated components because they strongly rely on the interactions among these numerous constituents. It focuses on in silico experiments rather than in vivo.

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

The minimum information about a simulation experiment (MIASE) is a list of the common set of information a modeller needs to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models.

Biosimulation is a computer-aided mathematical simulation of biological processes and systems and thus is an integral part of systems biology. Due to the complexity of biological systems simplified models are often used, which should only be as complex as necessary.

The ISCB Overton Prize is a computational biology prize awarded annually for outstanding accomplishment by a scientist in the early to mid stage of his or her career. Laureates have made significant contribution to the field of computational biology either through research, education, service, or a combination of the three.

COPASI is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.

GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene networks and other genetic constructs for genetic engineering and is based on the theory of formal languages.

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

JSBML is an open-source Java (API) for the SBML format. Its API strives to attain a strong similarity to the Java binding of the corresponding library libSBML, but is entirely implemented in Java and therefore platform independent. JSBML provides an elaborated abstract type hierarchy, whose data types implement or extend many interfaces and abstract classes from the standard Java library. In this way, JSBML integrates smoothly into existing Java projects, and provides methods to read, write, evaluate, and manipulate the content of SBML documents.

Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour of biological molecules or complexes that can adopt a large number of possible functional states.

Nicolas Le Novère is a British and French biologist. His research focuses on modeling signaling pathways and developing tools to share mathematical models.

Cell-based models are mathematical models that represent biological cells as discrete entities. Within the field of computational biology they are often simply called agent-based models of which they are a specific application and they are used for simulating the biomechanics of multicellular structures such as tissues. to study the influence of these behaviors on how tissues are organised in time and space. Their main advantage is the easy integration of cell level processes such as cell division, intracellular processes and single-cell variability within a cell population.

Mona Singh is an American computer scientist and an expert in computational molecular biology and bioinformatics. She is the Wang Family Professor in Computer Science in the Lewis-Sigler Institute for Integrative Genomics and the Department of Computer Science at Princeton University. Since 2021, she has been the Editor-in-Chief of the Journal of Computational Biology.

BEAST 2 is a cross-platform program for Bayesian analysis of molecular sequences. Using MCMC, it estimates rooted, timed phylogenies using a range of substitution and clock models, and a variety of tree priors. There is an associated tool, called BEAUTi, for setting up standard analyses. BEAST 2 is a complete re-write of the earlier BEAST program and as such draws on a large body of work. A notable feature of BEAST 2 is the packaging system which has simplified the process of implementing novel models.

Herbert M. Sauro is a Welsh biochemist who works in the field of metabolic control analysis and systems biology.

Smoldyn is an open-source software application for cell-scale biochemical simulations. It uses particle-based simulation, meaning that it simulates each molecule of interest individually, in order to capture natural stochasticity and yield nanometer-scale spatial resolution. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes in similar manners as in real biochemical systems.

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. PMC   9825722 . 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. (23 October 2023). "Tissue Forge: Interactive biological and biophysics simulation environment". PLOS Computational Biology. 19 (10): e1010768. Bibcode:2023PLSCB..19E0768S. doi: 10.1371/journal.pcbi.1010768 . PMC   10621971 . PMID   37871133.
  21. ↑ García García, Omar Rodrigo; Ortiz, Ramon; Moreno-Barbosa, Eduardo; D-Kondo, Naoki; Faddegon, Bruce; Ramos-Méndez, Jose (19 September 2024). "TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level". International Journal of Molecular Sciences. 25 (18): 10061. doi: 10.3390/ijms251810061 . PMC   11431975 . PMID   39337547.
  22. ↑ 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.
  23. ↑ 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.
  24. ↑ 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 .
  25. ↑ 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.
  26. ↑ 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.
  27. ↑ "Bifurcation Analysis".
  28. ↑ 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.
  29. ↑ 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.
  30. ↑ Sauro, Herbert. "Development Support".
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.