Dynamical modeling of biological systems is becoming increasingly widespread as people attempt to grasp biological phenomena in their full complexity and make sense of an accelerating stream of experimental data. We review a number of recent modeling studies that focus on systems specifically involving gene expression and regulation. These systems include bacterial metabolic operons and phase-variable piliation, bacteriophages T7 and lambda, and interacting networks of eukaryotic developmental genes. A wide range of conceptual and mathematical representations of genetic components and phenomena appears in these works. We discuss these representations in depth and give an overview of the tools currently available for creating and exploring dynamical models. We argue that for modeling to realize its full potential as a mainstream biological research technique the tools must become more general and flexible, and formal, standardized representations of biological knowledge and data must be developed.

中文翻译：

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遗传“代码”：遗传成分和网络的表示形式和动力学模型。

随着人们试图以完全复杂的方式掌握生物现象并理解不断加速的实验数据，生物系统的动态建模变得越来越普遍。我们回顾了许多最近的建模研究，这些研究专注于专门涉及基因表达和调控的系统。这些系统包括细菌代谢操纵子和阶段可变的菌毛，噬菌体T7和lambda以及真核发育基因的相互作用网络。这些工作中出现了广泛的遗传成分和现象的概念和数学表示。我们将深入讨论这些表示形式，并概述当前可用于创建和探索动力学模型的工具。