Modelling the Structure and Dynamics of Biological Pathways.
Modelling the Structure and Dynamics of Biological Pathways.
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生物途径的结构和动力学建模。
DOI：
10.1371/journal.pbio.1002530
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发表时间：
2016-08
期刊：
影响因子：
9.8
通讯作者：
Freeman TC
中科院分区：
文献类型：
--
作者：
O'Hara L;Livigni A;Theo T;Boyer B;Angus T;Wright D;Chen SH;Raza S;Barnett MW;Digard P;Smith LB;Freeman TC
有一个正式的图表，既总结了目前的生物途径知识和支持建模方法，解释和预测他们的行为的需要。在这里，我们提出了一个新的，免费提供的建模框架，其中包括一个生物学家友好的途径建模语言（mEPN），一个简单但复杂的方法来支持模型参数化使用现有的生物信息;随机流算法，模拟动态的途径活动;和3-D可视化引擎，有助于理解系统的动态的复杂性。我们提出了示例途径模型，说明了方法的力量来描绘各种各样的系统。这个社区页面提供了一个生物学家友好的方法，用于从文献中编译生物途径的详细图形模型，包括随后的参数化，用于动态模拟其活动。
There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system’s dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems. This Community Page presents a biologist-friendly method for compiling detailed graphical models of biological pathways from the literature, including their subsequent parameterization for use in dynamic simulations of their activity.