Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface
Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface
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DOI：
10.1093/bioinformatics/btw700
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发表时间：
2017-03-01
期刊：
影响因子：
5.8
通讯作者：
Andrews, Steven S.
中科院分区：
文献类型：
--
作者：
Andrews, Steven S.
动机：Smoldyn是一个空间和随机生化模拟器。它将每个感兴趣的分子视为连续空间中的单个粒子，模拟分子扩散，分子-膜相互作用和化学反应，所有这些都具有良好的准确性。本文介绍了几个新功能。结果：Smoldyn现在支持两种类型的基于规则的建模。这是一个非常方便的方法，和BioNetGen软件包与空间模拟的扩展，这是更好的复杂模型。Smoldyn还包括用于模拟表面结合分子和具有排除体积的分子的扩散的新算法。这两种方法在短时间步长的限制下都是精确的，在长时间步长的限制下也相当好。此外，Smoldyn支持单分子跟踪模拟。最后，Smoldyn源代码可以通过C/C++语言库接口访问。
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 is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C++ language library interface.