COMPUTATIONAL INFRASTRUCTURE FOR VIRTUAL CELL

这个子项目是许多利用 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， 因此可在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 细胞结构和功能由一系列相互依赖的生化反应和过程决定，这些反应和过程在空间上以非均匀的方式分布在细胞内。虚拟细胞是一个计算环境，它允许一种通用的方法来模拟空间组织和相互依赖的化学过程，决定细胞功能。这项新技术的目的是让实验细胞生物学家能够创建模型，这些模型可以作为细胞内动力学数值模拟的输入。在幕后，需要进行复杂的转换，以从生物模型和实验模型构建相应的数学模型。 应用. 这些包括图论方法，符号操作的方程和其他算法，可以最佳地利用问题的结构。 这些算法的新版本针对存储在数据库中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，并使用回归测试对大量具有已知解的模型进行测试。 当我们进行虚拟单元的开发时，我们采用了新的建模抽象，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.