使用不同层次的表示法模拟细胞周期
Modelling Cell Cycle using Different Levels of Representation
摘要：
了解生物系统的行为需要复杂的体外和体内实验环境，这在时间和资源方面都需要很高的成本。数学模型的使用使研究人员能够对生物系统进行计算机模拟，这被称为计算机实验，以相当低的成本获得有关系统行为的重要见解和预测。计算机可视化是这种方法的一个重要组成部分，因为它提供了系统行为的真实表示。我们定义了一个正式的方法来模拟生物系统使用不同层次的表示：一个纯粹的正式表示，我们称之为分子水平，模型的生化动力学系统;可视化为导向的表示，我们称之为视觉水平，提供生物系统在更高层次的组织视图，并配备了必要的空间信息，以产生适当的可视化。我们选择空间CLS，一个形式语言属于类的循环序列的演算，作为形式主义建模的所有代表性的水平。我们说明我们的方法使用芽殖酵母细胞周期作为案例研究。
英文摘要：
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study.
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