Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface

@article{Andrews2017SmoldynPS,
  title={Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface},
  author={Steven S. Andrews},
  journal={Bioinformatics},
  year={2017},
  volume={33 5},
  pages={710-717}
}
Motivation Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Results Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which… CONTINUE READING
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