PySCeS
| Initial release | February 15, 2005 |
|---|---|
| Stable release | 1.0.2
/ May 1, 2022 |
| Written in | Python, C++, C, FORTRAN |
| Engine | |
| Operating system | Linux, macOS and Microsoft Windows |
| Platform | Python |
| License | BSD License |
| Website | pysces |
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PySCeS.[1] is a Python-based open-source simulator for cellular systems. The software was originally developed by Brett Olivier in the early 2000s[2]. PySCeS was the first biochemical simulation software package written in Python. As well as being able to run time-dependent simulations, PySCeS also has extensive support for metabolic control analysis. The software runs on all major platforms, Windows, Mac OS, and Linux.
Capabilities
For a list of capabilities, the reader is referred to the primary and secondary sources at the end of the page.
Applications
PySCeS has been widely used in the systems biology community for doing research in systems biology modeling:
- Pillay et al.[3] used PySCeS to build a model of redox signaling.
- Kerkhoven et al. used PySCeS to study the handling of uncertainty in dynamic models of *Trypanosoma brucei*.
As of October 2022, the original PySCeS publication has received 226 citations, according to Google Scholar.
Notability
- PySCeS was the first Python-based tool for doing systems biology modeling.
- PySCeS was also the first tool that implemented extensive support for structural analysis[4] of the stoichiometry matrix.
A number of reviews and commentaries have been written that discuss PySCeS:
- Sauro and Bergmann[5] discuss a variety of simulation platforms with a specific section on PySCeS.
- Schölzel et al[6] discuss a variety of text-based languages, including PySCeS.
- Vallabhajosyula et al[7], discuss the stoichiometry analysis algorithms used by PySCeS.
See also
References
- ↑ Olivier, Brett; Rohwer, Johann; Hofmeyr, Jan-Hendrik (2005). "Modelling cellular systems with PySCeS". Bioinformatics. 21 (4): 560–561. doi:10.1093/bioinformatics/bti046. PMID 15454409.
- ↑ "PySCeS: The Python Simulator for Cellular Systems". pysces.sourceforge.net.
- ↑ Pillay, Ché S.; Eagling, Beatrice D.; Driscoll, Scott R.E.; Rohwer, Johann M. (July 2016). "Quantitative measures for redox signaling". Free Radical Biology and Medicine. 96: 290–303. doi:10.1016/j.freeradbiomed.2016.04.199. PMID 27151506.
- ↑ Reder, Christine (November 1988). "Metabolic control theory: A structural approach". Journal of Theoretical Biology. 135 (2): 175–201. Bibcode:1988JThBi.135..175R. doi:10.1016/S0022-5193(88)80073-0. PMID 3267767.
- ↑ Sauro, Herbert M.; Bergmann, Frank T. (2010). "Software Tools for Systems Biology". Systems Biomedicine: 289–314. doi:10.1016/B978-0-12-372550-9.00012-2. ISBN 9780123725509.
- ↑ Schölzel, Christopher; Blesius, Valeria; Ernst, Gernot; Dominik, Andreas (December 2021). "Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective". npj Systems Biology and Applications. 7 (1): 27. doi:10.1038/s41540-021-00182-w. PMC 8175692 Check
|pmc=value (help). PMID 34083542 Check|pmid=value (help). - ↑ Vallabhajosyula, R. R.; Chickarmane, V.; Sauro, H. M. (1 February 2006). "Conservation analysis of large biochemical networks". Bioinformatics. 22 (3): 346–353. doi:10.1093/bioinformatics/bti800. PMID 16317075.
External links
- PySCeS at sourceforge.net
- PySCeS at GitHub
This article "PySCeS" is from Wikipedia. The list of its authors can be seen in its historical and/or the page Edithistory:PySCeS. Articles copied from Draft Namespace on Wikipedia could be seen on the Draft Namespace of Wikipedia and not main one.
