MULTI-PHYSICS LAYER

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 为了支持所需的灵活性和未来的扩展性，我们的广义PSE架构，一个额外的物理建模层将被引入。 当前的虚拟细胞具有从特定领域的定量过程描述（由化学、电生理和运输机制组成的生理模型）和用户指定的假设直接转换为纯数学模型的功能。 从生物学过程到数学的这种转变中隐含着对特定物理近似、几何映射、时间尺度和基本物理定律的选择。 添加额外的建模域以及测量设备的显式模型（例如虚拟实验）需要一个中间物理层，其中所有过程（和方程）都是显式的，但仍然与过程描述一一对应。 从相互连接的“物理设备”到可解方程组的转换，然后从物理上一致的模型的制定中分离出来。 物理一致性的语义沿着数学一致性的语义嵌入在这一层中。 我们将定义这个物理层的语义和操作，并提供一个参考实现（允许其他表示，如CellML和Modelica）。 这一层的规范为专门和复杂的数学转换提供了空间，以将物理/数学系统转换为可解形式。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. In order to support the required flexibility and future extensibility of our generalized PSE architecture, an additional physical modeling layer will be introduced. The current Virtual Cell features a direct transformation from a domain-specific quantitative process description (the physiological model consisting of chemical, electrophysiological, and transport mechanisms) and user specified assumptions directly to a purely mathematical model. Implicit in this transformation from biological processes to mathematics are the choice of specific physical approximations, geometric mappings, time scales, and the underlying physical laws. The addition of additional modeling domains as well as explicit models of measurement devices (e.g. virtual experiments) call out for an intermediate physical layer where all processes (and equations) are explicit, but still map one-to-one with the process descriptions. The translation from interconnected "physical devices" to solvable systems of equations is then isolated from the formulation of a physically consistent model. Embedded in this layer are the semantics of physical consistency along with those of mathematical consistency. We will define the semantics and operations of this physical layer and provide a reference implementation (allowing for alternate representations such as CellML and Modelica). The specification of this layer provides room for specialized and sophisticated mathematical transformations to transform the physical/mathematical systems into a solvable form.