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Automated model-driven generation of software components for the simulation of epithelial tissues

机译:由模型驱动的软件组件的自动生成,用于模拟上皮组织

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Quantitative in silico modeling is a powerful means to enhance our understanding of complex biological systems. Accordingly, intuitive and flexible computational tools are needed to support the development of such models. We previously developed the platform EPISIM for graphical modeling and simulation of cellular behavior in epithelia. In this work we demonstrate how computationally efficient software components for epithelial tissue simulations can be automatically generated. We introduce a model-driven workflow to generate extendable and exchangeable software components for both the modeling and the simulation of epithelial tissues. We distinguish two levels of abstraction in our workflow and thus two kinds of models: (i) the meta-model of our modeling language and (ii) particular systems biological cell behavioral models. The model-driven component generation allows optimization of the underlying code and the automated integration in our EPISIM platform. We evaluated the computational performance and the correctness of the generated software components. In this work we focus on the evaluation of the computational performance. It could be shown that the execution time increases nearly linearly with the size of the generated component's underlying model.
机译:定量计算机模拟是一种增强我们对复杂生物系统的理解的有力手段。因此,需要直观且灵活的计算工具来支持这种模型的开发。我们之前开发了平台EPISIM,用于上皮细胞行为的图形化建模和仿真。在这项工作中,我们演示了如何自动生成用于上皮组织模拟的具有计算效率的软件组件。我们引入了模型驱动的工作流程,以生成可扩展和可交换的软件组件,以用于上皮组织的建模和仿真。我们在工作流程中区分了两个抽象层次,因此区分了两种模型:(i)我们的建模语言的元模型和(ii)特定系统的生物细胞行为模型。通过模型驱动的组件生成,可以优化基础代码并在我们的EPISIM平台中进行自动集成。我们评估了生成的软件组件的计算性能和正确性。在这项工作中,我们专注于计算性能的评估。可以证明,执行时间几乎随生成的组件的基础模型的大小线性增长。

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