Smoldyn information

Smoldyn
Original author(s)	Steve Andrews
Initial release	July 1, 2003; 20 years ago
Stable release	2.71 / February 6, 2023; 15 months ago
Repository	github.com/ssandrews/Smoldyn
Written in	C, C++, Python
Operating system	Linux, macOS and Windows
Type	Simulation software
License	LGPL
Website	www.smoldyn.org

Smoldyn is an open-source software application for cell-scale biochemical simulations.^[1]^[2] 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.

^ Andrews, Steven S.; Addy, Nathan J.; Brent, Roger; Arkin, Adam P. (2010). "Detailed simulations of cell biology with Smoldyn 2.1". PLOS Comput. Biol. 6 (3): e1000705. Bibcode:2010PLSCB...6E0705A. doi:10.1371/journal.pcbi.1000705. PMC 2837389. PMID 20300644.
^ Andrews, Steven S. (2017). "Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction, and a library interface". Bioinformatics. 33 (5): 710–717. doi:10.1093/bioinformatics/btw700. PMID 28365760.

[Andrews_Arkin_2010-1] Andrews, Steven S.; Addy, Nathan J.; Brent, Roger; Arkin, Adam P. (2010). "Detailed simulations of cell biology with Smoldyn 2.1". PLOS Comput. Biol. 6 (3): e1000705. Bibcode:2010PLSCB...6E0705A. doi:10.1371/journal.pcbi.1000705. PMC 2837389. PMID 20300644.

[Andrews_2017-2] Andrews, Steven S. (2017). "Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction, and a library interface". Bioinformatics. 33 (5): 710–717. doi:10.1093/bioinformatics/btw700. PMID 28365760.

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