【作者】 陈晟；

【导师】 骆清铭；

【作者基本信息】 华中科技大学 ， 物理电子学， 2004， 硕士

【摘要】 分子生物学领域的进步,基因组及相关计划的进展,使得系统生物学逐渐成为生命科学研究中的热点。为了从系统层次理解生命过程,我们必须研究从细胞到有机体各个层次的结构、功能及其相关的动力学特性。目前系统生物学研究多采用实验和仿真交替实施互为验证的方式。改变系统结构和参数来分析系统的动力学特性,难以通过实际的生物实验完成。因此,建立生物系统模型,通过仿真获得对生物系统的理解,预测生物系统行为,成为目前系统生物学研究引人关注的内容之一。本文设计了一种应用于系统生物学的编程语言——B语言,并开发了B语言的解释器及仿真环境。B语言的建模语法根据系统生物学标记语言设计,符合当前通行标准,并且B语言具有交互性解释型编程语言的特征,配合构建的仿真环境,就能方便的对模型进行仿真和计算。文中还分别用Matlab和B语言对一个典型的最小钙振荡模型进行仿真,通过比较仿真方式和结果,证实B语言在保证结果准确无误的前提下大大提高了系统生物学研究者的工作效率。在系统的设计过程中,我们采用了面向对象的程序设计思想,通过编译器自动生成工具JavaCC构造基于Java的B语言解释器,从而保证了B语言具有良好的通用性和可扩展性。此外我们还借助一些开源项目来构建仿真环境,既保证了仿真的方便性和直观性,又能适应B语言后续开发不断扩充的需求。更多还原

【Abstract】 The progress of molecular biology and the development of genome saw systems biology becoming the hotspot of life science. To understand the biological process systematically, it is necessary to research the anatomy, physiology and dynamics from cell to organism. In current research of systems biology, experiment, simulation and rich talk between them are widely used to give a good understanding. As we know, it is difficult to analyze the dynamics of biological system by changing its parameters or structure biologically. So modeling, simulation and forecasting become promising approaches for systems biology, attracting extensive researches so far.In this thesis, B language—a programming language applied to systems biology is designed with its interpreter and simulator developed at the same time. The modeling grammar of B language is compatible with Systems Biology Markup Language (SBML), current actual standard. As an interactive interpreting programming language, B language, combined with its simulator, provided a convenient way for calculation of the complex biological model. A classic model, minimal model for signal-induced Ca2+ oscillations, is simulated with Matlab and B language respectively to compare the simulation steps and results. The conclusion demonstrates that B language is more appropriate for systems biology research.Object-Oriented Design (OOD) and compiler generator JavaCC were introduced, which provided guarantee for the scalability of B language to some extent. Besides, some open source projects are incorporated in the developing of the simulator, which facilitate not only the development itself but also the revolution of B language while requirement increases.更多还原