GENERALIZED ARCHITECTURE FOR MODELING AND SIMULATION

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 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，并为分析和互操作性提供额外的工具。根据我们在开发现有虚拟细胞方面的经验，我们现在准备为细胞生理的空间和非空间建模和仿真定义一个通用的建模和仿真体系结构。现有的虚拟单元的分层建模方法将被很好地概括为抽象层次的规范，具有清晰的语义、清晰的接口和灵活的表示和实现。我们将在这些抽象数据类型上定义许多抽象服务，并提供数据(模型、数据、数学)和服务(解算器、分析器、转换器、层之间的映射)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(如SBML、CellML、VCML)和工具(现有和第三方解算器、模型分析、数据分析和拟合)可以集成到建模过程中。将创建高级建模本体，以形式化语义定义，引用或导入适当的领域特定本体，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.