MULTI-PHYSICS LAYER

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。 为了支持我们的通用PSE体系结构所需的灵活性和未来的可扩展性，将引入一个额外的物理建模层。当前的虚拟细胞的特点是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粹的数学模型。在从生物过程到数学的这种转变中，隐含着对具体物理近似、几何映射、时间尺度和潜在物理定律的选择。附加建模域以及测量设备的显式模型(例如，虚拟实验)的添加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。然后，从相互关联的“物理设备”到可解的方程系统的转换从物理上一致的模型的公式中分离出来。嵌入这一层的是物理一致性的语义以及数学一致性的语义。我们将定义此物理层的语义和操作，并提供参考实现(允许使用CellML和Modelica等替代表示)。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的形式。

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. 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.