A multi-algorithm, multi-timescale method for cell simulation
A multi-algorithm, multi-timescale method for cell simulation
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DOI：
10.1093/bioinformatics/btg442
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发表时间：
2004-03-01
期刊：
影响因子：
5.8
通讯作者：
Tomita, M
中科院分区：
文献类型：
--
作者：
Takahashi, K;Kaizu, K;Tomita, M
动机：细胞生物学中的许多重要问题需要考虑功能模块之间的密集非线性相互作用。计算机模拟在理解细胞过程中的重要性现在被广泛接受，并且已经设计了用于研究某些子系统的各种模拟算法。其中许多已经被广泛使用，并建立了大量的模型，这些现有的形式主义。一个显着的计算挑战是，我们如何可以集成这样的子细胞模型运行在不同类型的算法，以构建更高的阶models.Results：一个模块化的，面向对象的仿真元算法的基础上的离散事件调度和Hermite多项式插值已开发和实施。结果表明，这种新方法可以有效地处理许多组件驱动的不同算法和不同的时间尺度。这个模拟框架的效用进一步证明了一个“复合”热冲击响应模型，结合了Gillespie-Gibson随机算法和确定性微分方程。在性能上获得了显著的改进，而没有显著的精度缺点。耦合谐振子的多时标演示也显示。
Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models.Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a 'composite' heat-shock response model that combines the Gillespie-Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown.