A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation
A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation
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DOI：
10.14326/abe.3.50
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发表时间：
2014-01-01
影响因子：
1
通讯作者：
Kitano, Hiroaki
中科院分区：
文献类型：
--
作者：
Asai, Yoshiyuki;Abe, Takeshi;Kitano, Hiroaki
已经设计了用于描述系统生物学和生理学领域计算模型的专用语言，例如系统生物学标记语言（SBML），CellML和生理层次结构标记语言（PHML），以增强研究人员之间有效的模型和共享开发大型多级模型。每种语言都有自己的专业。通过结合其中两种语言，即。 e。 SBML用于说明用于表达细胞上动力学的亚细胞现象和PHML的SBML，已开发出一种新技术来描述多级生物生理系统的模型。为了实际使用上述语言，需要进行合并的软件应用程序提供直观的图形用户界面。从2011年开始，已经开发了一个名为Physiodesigner的多功能平台，用于基于PHML的生理系统的多级建模。在本文中，我们专注于使用SBML-PHML杂交的新开发的Physiodesigner和PHML的区别特征，用于开发多级生物生理模型。
Specialized languages used for describing computational models in the field of systems biology and physiology, such as Systems Biology Markup Language (SBML), CellML, and Physiological Hierarchy Markup Language (PHML), have been devised to enhance effective model reuse and sharing among researchers for developing large, multilevel models. Each language has its own specialty. By combining two of these languages, i. e. SBML for illustrating subcellular phenomena and PHML for expressing supracellular dynamics, a novel technology has been developed to describe models of multilevel biophysiological systems. For practical use of the aforementioned languages, consolidated software applications providing intuitive graphical user interfaces are necessary. Starting from 2011, a versatile platform called PhysioDesigner has been developed for multilevel modeling of physiological systems based on PHML. In this article, we focus on the newly developed distinguishing features of PhysioDesigner and PHML for the development of multilevel biophysiological models using SBML-PHML hybridization.