GENERALIZED ARCHITECTURE FOR MODELING AND SIMULATION

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 虚拟单元的持续发展需要能够优雅地扩展所支持的建模域，以及提供用于分析和互操作性的附加工具。 借鉴我们的经验与现有的虚拟细胞的发展，我们现在准备定义一个通用的架构，为空间和非空间建模和模拟细胞生理学的建模和模拟。 将现有的虚拟单元分层建模方法推广为语义清晰、接口清晰、表示和实现灵活的抽象层规范。 我们将在这些抽象数据类型上定义一些抽象服务，并提供数据（模型，数据，数学）和服务（求解器，分析器，翻译器，层间映射）的参考实现。 通过使用一组可扩展的转换器和适配器，现有的数据格式（例如SBML，CellML，VCML）和工具（现有和第三方求解器，模型分析，数据分析和拟合）可以集成到建模过程中。 将创建一个高级建模本体，以形式化语义定义，引用或导入适当的特定领域本体，如SBO。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The continued evolution of the virtual cell requires the ability to gracefully extend the supported modeling domains as well as provide additional tools for analysis and interoperability. Drawing on our experience with the development of the existing Virtual Cell, we are now poised to define a generalized architecture for modeling and simulation for spatial and non-spatial modeling and simulation of cell physiology. The existing layered modeling approach of the Virtual Cell will be considerably generalized into a specification of abstract layers with clear semantics, clear interfaces and flexible representation and implementations. We will define a number of abstract services on these abstract data types and provide reference implementations of both data (models, data, mathematics) and services (solvers, analyzers, translators, mappings between layers). Through the use of an extensible set of translators and adapters, existing data formats (e.g. SBML, CellML, VCML) and tools (exiting and third party solvers, model analysis, data analysis and fitting) can be integrated within the modeling process. A high level modeling ontology will be created to formalize the semantic definitions, referencing or importing appropriate domain specific ontologies such as SBO.