Mendes Pedro, Hoops Stefan, Sahle Sven, Gauges Ralph, Dada Joseph, Kummer Ursula
Manchester Centre for Integrative Systems Biology, University of Manchester, UK.
Methods Mol Biol. 2009;500:17-59. doi: 10.1007/978-1-59745-525-1_2.
Computational modeling and simulation of biochemical networks is at the core of systems biology and this includes many types of analyses that can aid understanding of how these systems work. COPASI is a generic software package for modeling and simulation of biochemical networks which provides many of these analyses in convenient ways that do not require the user to program or to have deep knowledge of the numerical algorithms. Here we provide a description of how these modeling techniques can be applied to biochemical models using COPASI. The focus is both on practical aspects of software usage as well as on the utility of these analyses in aiding biological understanding. Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis (including metabolic control analysis), global optimization, parameter estimation, and stochastic simulation. The examples used are all published models that are available in the BioModels database in SBML format.
生化网络的计算建模与模拟是系统生物学的核心，这包括许多有助于理解这些系统如何运作的分析类型。COPASI是一个用于生化网络建模与模拟的通用软件包，它以方便的方式提供了许多此类分析，用户无需编程或深入了解数值算法。在此，我们描述如何使用COPASI将这些建模技术应用于生化模型。重点在于软件使用的实际方面以及这些分析在辅助生物学理解方面的效用。描述了稳态和时间进程模拟、化学计量分析、参数扫描、灵敏度分析（包括代谢控制分析）、全局优化、参数估计和随机模拟的实际示例。所使用的示例均为已发表的模型，可在BioModels数据库中以SBML格式获取。
