COMPUTATIONAL INFRASTRUCTURE FOR VIRTUAL CELL

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。 细胞的结构和功能由一系列相互依赖的生化反应和过程决定，这些反应和过程在细胞内以非均质的方式在空间上分布。虚拟细胞是一种计算环境，它允许对决定细胞功能的空间组织和相互依赖的化学过程进行建模的一般方法。这项新技术旨在让实验细胞生物学家能够创建模型，作为细胞内动力学的数值模拟的输入。在幕后，需要进行复杂的转换，以从生物模型和实验应用程序构建相应的数学模型。这些方法包括图论方法、方程的符号处理和其他可以最大限度地利用问题结构的算法。这些算法的新版本将针对数据库中存储的数千个模型进行回归测试。这些数学模型的数值解也在不断开发中，并使用回归测试对一大组具有已知解的模型进行测试。随着虚拟单元的开发，我们吸收了新的建模抽象、新的数学形式、新的数值技术和新的模型分析技术。

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. Cellular structure and function is determined by an array of interdependent biochemical reactions and processes, spatially distributed in a non-homogenous fashion within the cell. The Virtual Cell is a computational environment that allows a general approach for modeling the spatially organized and interdependent chemical processes that determine cell function. This new technology is designed to be accessible to the experimental cell biologist to create models that can serve as input to a numerical simulation of intracellular dynamics. Behind the scenes, there are complex transformations required to construct the corresponding mathematical model from the biological model and an experimental application. These consist of graph theoretic approaches, symbolic manipulation of equations and other algorithms that can optimally take advantage of the structure of the problem. New versions of these algorithms are regression tested against the thousands of models stored in the database. The numerical solution of these mathematical models are also under continuous development, and are tested using regression testing against a large set of models with known solutions. As we proceed in development of the Virtual Cell, we incorporate new modeling abstractions, new mathematical formalisms, new numerical techniques and new model analysis techniques.