PySB
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| Initial release | May 15, 2019 |
|---|---|
| Stable release | 1.14
/ August 29, 2022 |
| Written in | Python |
| Engine | |
| Operating system | Linux, macOS and Microsoft Windows |
| Platform | Python |
| License | BSD License |
| Website | pysb |
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PySB[edit]
PySB..[1] is a Python-based open-source simulator for cellular systems developed by Carlos Lopez. The primary capability of pySB than makes it stand out from other similar simulators is that it supports rule-based modeling[2]. The software runs on all major platforms, Windows, Mac OS, and Linux. PySB is also discussed at Multi-state modeling of biomolecules.
Capabilities[3][edit]
- Can be used to describe rule-based models of complex biochemical pathways, particularly signaling pathways.
- Can be used to create model libraries based on macros to reuse.
- Uses standard python sci-py numerical libraries for carrying out simulations.
Applications of pySB[edit]
pySB has been used in a variety of research projects. The following lists a small number of those studies (out of a total of 230 mentions in the scientific literature (as of Oct 2022).
- Studies on substrate selectivity in cyclooxygenase-2[4]
- Information discrimination in T-cell signaling[5]
- Inverted control of eukaryotic gene expression[7]
- Construction of Cellular Responses and Global Drug Mechanisms of Action[8]
These have all been impactful studies (Google Scholar) and indicate that pySB is being used in a variety of important research areas.
Notability[edit]
There are a number of distinguishing features of pySB that make it standout from other similar cellular modeling platforms:
- PySB is the only python-based simulation package for systems biology that supports rule-based modeling.
- PySB also allows users to divide models into modules and to call libraries of reusable elements (macros) that encode standard biochemical actions.
A number of reviews and commentaries have been written that discuss pySB:
- Slater[11]. describes in detail the pros and cons of a variety of rule-based languages and platforms, including pySB
- Mitra and Hlaveck[12] briefly discuss the importance of pySB, where they state: "Another package of note is PySB which has support for BNGL"
- Chicklet et al[13], discuss at length a variety of rule-based modeling platforms but particularly pySB.
SBML Support[edit]
pySB is able to export SBML in flattened form[14]. That is, the rule-based model is converted into explicit reactions. This means that the rule-based formalism is not preserved.
For import, pySB converts the SBML into BioNetGen first using BioNetGen application. pySB then imports the BioNetGen format using the pySB BioNetGen importer. This means import is limited by the import capabilities of BioNetGen[15]
See also[edit]
References[edit]
- ↑ Lopez, Carlos F; Muhlich, Jeremy L; Bachman, John A; Sorger, Peter K (January 2013). "Programming biological models in Python using PySB". Molecular Systems Biology. 9 (1): 646. doi:10.1038/msb.2013.1. PMC 3588907. PMID 23423320.
- ↑ Chylek, Lily A.; Harris, Leonard A.; Tung, Chang‐Shung; Faeder, James R.; Lopez, Carlos F.; Hlavacek, William S. (January 2014). "Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems". WIREs Systems Biology and Medicine. 6 (1): 13–36. doi:10.1002/wsbm.1245. PMC 3947470. PMID 24123887.
- ↑ "readthedocs for pysb".
- ↑ Mitchener, Michelle M.; Hermanson, Daniel J.; Shockley, Erin M.; Brown, H. Alex; Lindsley, Craig W.; Reese, Jeff; Rouzer, Carol A.; Lopez, Carlos F.; Marnett, Lawrence J. (6 October 2015). "Competition and allostery govern substrate selectivity of cyclooxygenase-2". Proceedings of the National Academy of Sciences. 112 (40): 12366–12371. Bibcode:2015PNAS..11212366M. doi:10.1073/pnas.1507307112. PMC 4603459. PMID 26392530.
- ↑ Ganti, Raman S.; Lo, Wan-Lin; McAffee, Darren B.; Groves, Jay T.; Weiss, Arthur; Chakraborty, Arup K. (20 October 2020). "How the T cell signaling network processes information to discriminate between self and agonist ligands". Proceedings of the National Academy of Sciences. 117 (42): 26020–26030. Bibcode:2020PNAS..11726020G. doi:10.1073/pnas.2008303117. PMC 7585026 Check
|pmc=value (help). PMID 33020303 Check|pmid=value (help). - ↑ Perry, Nicole A.; Kaoud, Tamer S.; Ortega, Oscar O.; Kaya, Ali I.; Marcus, David J.; Pleinis, John M.; Berndt, Sandra; Chen, Qiuyan; Zhan, Xuanzhi; Dalby, Kevin N.; Lopez, Carlos F.; Iverson, T. M.; Gurevich, Vsevolod V. (15 January 2019). "Arrestin-3 scaffolding of the JNK3 cascade suggests a mechanism for signal amplification". Proceedings of the National Academy of Sciences. 116 (3): 810–815. Bibcode:2019PNAS..116..810P. doi:10.1073/pnas.1819230116. PMC 6338856. PMID 30591558.
- ↑ Park, Heungwon; Subramaniam, Arvind R. (18 September 2019). "Inverted translational control of eukaryotic gene expression by ribosome collisions". PLOS Biology. 17 (9): e3000396. doi:10.1371/journal.pbio.3000396. PMC 6750593 Check
|pmc=value (help). PMID 31532761. - ↑ Norris, Jeremy L.; Farrow, Melissa A.; Gutierrez, Danielle B.; Palmer, Lauren D.; Muszynski, Nicole; Sherrod, Stacy D.; Pino, James C.; Allen, Jamie L.; Spraggins, Jeffrey M.; Lubbock, Alex L. R.; Jordan, Ashley; Burns, William; Poland, James C.; Romer, Carrie; Manier, M. Lisa; Nei, Yuan-wei; Prentice, Boone M.; Rose, Kristie L.; Hill, Salisha; Van de Plas, Raf; Tsui, Tina; Braman, Nathaniel M.; Keller, M. Ray; Rutherford, Stacey A.; Lobdell, Nichole; Lopez, Carlos F.; Lacy, D. Borden; McLean, John A.; Wikswo, John P.; Skaar, Eric P.; Caprioli, Richard M. (3 March 2017). "Integrated, High-Throughput, Multiomics Platform Enables Data-Driven Construction of Cellular Responses and Reveals Global Drug Mechanisms of Action". Journal of Proteome Research. 16 (3): 1364–1375. doi:10.1021/acs.jproteome.6b01004. PMID 28088864.
- ↑ Blinov, M. L.; Faeder, J. R.; Goldstein, B.; Hlavacek, W. S. (22 November 2004). "BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains". Bioinformatics. 20 (17): 3289–3291. doi:10.1093/bioinformatics/bth378. PMID 15217809.
- ↑ Boutillier, Pierre; Maasha, Mutaamba; Li, Xing; Medina-Abarca, Héctor F; Krivine, Jean; Feret, Jérôme; Cristescu, Ioana; Forbes, Angus G; Fontana, Walter (1 July 2018). "The Kappa platform for rule-based modeling". Bioinformatics. 34 (13): i583–i592. doi:10.1093/bioinformatics/bty272. PMC 6022607. PMID 29950016.
- ↑ Slater, Ted (February 2014). "Recent advances in modeling languages for pathway maps and computable biological networks". Drug Discovery Today. 19 (2): 193–198. doi:10.1016/j.drudis.2013.12.011. PMID 24444544.
- ↑ Mitra, Eshan D.; Hlavacek, William S. (December 2019). "Parameter estimation and uncertainty quantification for systems biology models". Current Opinion in Systems Biology. 18: 9–18. doi:10.1016/j.coisb.2019.10.006. PMC 7384601 Check
|pmc=value (help). PMID 32719822 Check|pmid=value (help). - ↑ Chylek, Lily A.; Harris, Leonard A.; Tung, Chang‐Shung; Faeder, James R.; Lopez, Carlos F.; Hlavacek, William S. (January 2014). "Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems". WIREs Systems Biology and Medicine. 6 (1): 13–36. doi:10.1002/wsbm.1245. PMC 3947470. PMID 24123887.
- ↑ "pySB Export".
- ↑ "pySB Import".
External links[edit]
This article "PySB" is from Wikipedia. The list of its authors can be seen in its historical and/or the page Edithistory:PySB. Articles copied from Draft Namespace on Wikipedia could be seen on the Draft Namespace of Wikipedia and not main one.
