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Programming with models: modularity and abstraction provide powerful capabilities for systems biology

机译:使用模型编程:模块化和抽象为系统生物学提供强大的功能

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摘要

Mathematical models are increasingly used to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fundamental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling generic properties of biological processes to be specified independently of specific instances. These, in turn, require models to be represented as programs rather than as datatypes. Programmable modularity and abstraction enables libraries of modules to be created, which can be instantiated and reused repeatedly in different contexts with different components. We have developed a computational infrastructure that accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously.
机译:数学模型越来越多地用于理解表型如何从分子相互作用系统中出现。然而,它们当前作为整体式方程组的构造提出了前进的根本障碍。克服这一点需要模块化,从而可以独立指定子系统并进行增量组合,还可以进行抽象化,从而可以独立于特定实例指定生物过程的通用属性。反过来,这些要求将模型表示为程序而不是数据类型。可编程的模块性和抽象性使得可以创建模块库,这些模块库可以在具有不同组件的不同上下文中被实例化和重复使用。我们已经开发出可以实现此目的的计算基础架构。我们在这里展示了为什么需要这样的功能,实现这些功能需要什么,以及使用它们以前无法完成的工作。

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