摘 要：摘 要：系统生物学倡导利用系统论的思想和方法，从整体的高度分析、研究生命的复杂特性。这一点与实验生物学仅关注某一个或者某一些生物大分子是迥然不同的。系统生物学既要同时考虑多个层次、多种类型的生物信息，还要考虑时间因素。由于系统特性是由于不同组成部分、不同层次间相互作用而“涌现”出的新性质，因此，如果只是针对组成部分或单一层次的分析并不能真正准确地预测整体或高层次的行为。如何通过研究和整合去发现和理解“涌现”出的新的系统性质，是系统生物学面临的一个根本性的挑战。为了应对这一挑战，系统生物学，特别是计算系统生物学必须建立有效的方法，通过整合系统各个层次的信息，建立可反映该系统目前已知或已可测量的性质的物理、数学模型，并通过这样的模型来研究或预测目前还未知晓的系统性状。可以说：建模是系统生物学的最重要的研究手段之一。目前，生命科学的研究正逐步由对单一现象、单一过程的机械论式的描述型研究转向运用高通量实验技术获取海量生物信息，并在这些生物信息基础上建立物理、数学模型，最终通过建模与实验相接合的研究手段来定量阐述生命现象的本质规律。由于建模方法在系统生物学研究中的重要性，本文将对一些主要的建模类型，如定性建模方法；基于约束的建模方法；基于常微分/ 偏微分方程的定量建模和基于随机微分方程的定量建模方法等等分别予以简要介绍。
关键词：系统生物学；建模方法；模拟
Abstract: Abstract: Systems biology is the study of a complex biological system, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life. Instead of analyzing individual genes, proteins, components or aspects of complex biological system, systems biology focuses on all the information from different level of system even together with the factor of time. Because the form and functions of a system result from interactions among all the components of system, we call these properties and functions that arise from the interacting parts in a system "emergent properties". The concept of emergent properties is central to the study of systems. Any function performed by a system that is not the result of a single part in the system, but rather is the result of interacting parts in the system, is an emergent property. Currently, finding new methods, which can integrate whole information of all individual components or aspects of complex biological system, to study the "emergent properties" of a complex biological system effectively is still a big challenge. Systems biology or computational systems biology should integrate all information from different system levels and base on it to set up modeling and simulation methods to demonstrate the known functions and predict unknown properties of system. From this point of view, modeling and simulation methods and tools play a central role and shall be the focus of systems biology studies. Because of its essentiality, the main methodologies of modeling and simulation methods in systems biology, such as Qualitative models, Constrained models, Deterministic ODE/PDE models and Stochastic Differential Equations Models, are introduced in this review article.
Key words: systems biology; modeling; simulation
