SGER: Developing a Database Supporting Cell Biology Modeling - A Feasibility Study

项目摘要虚拟细胞项目旨在开发一个为模拟细胞生物学过程而设计的框架，该框架包含数学、物理和数值作为一个透明的基础设施。该项目的成功实施将使细胞生物学家能够构建和测试模型，以帮助理解他们的实验。该项目的一个重要补充将是一个包含模型、图像以及生化和电生理数据的数据库；这样的数据库不仅将支持虚拟细胞，而且将独立地成为细胞生物界的宝贵资源。这项提议旨在研究开发一个能够支持虚拟细胞的数据库的可行性。我们将尝试建立一个数据库，其中包括描述生化和电生理反应的一组方程，从显微图像得出的细胞几何形状，以及细胞间隔区的空间关系。在这项可行性研究期间，我们的数据收集将主要集中在我们自己的实验室已有的数据上。此外，我们将尝试将有限的一组已发表的反应动力学、电生理数据、图像和模型汇编、分组并存储到数据库中。总体而言，我们与数据库建设相关的研究重点将是研究组织各种不同种类的计算数据集的可行性，以便这些数据可以无缝地集成到演示复杂细胞生物化学过程的计算模型的生产和评估中。虚拟细胞项目的影响是彻底改变了细胞生物学家研究活体复杂功能和行为的方式。成功实施我们的可行性研究将使我们能够制定一个较长期的研究框架。一旦成功，长期研究框架将允许科学家观察和检查化学和运动学变化的详细步骤，而无需进行实际实验。我们预计，这样的资源在实验室和课堂上都将非常有用。

PROJECT SUMMARY The Virtual Cell Project aims at developing a framework designed for modeling cell biological processes that contains the mathematics, physics and numerics as a transparent infrastructure. A successful implementation of the project will make it possible for cell biologists to construct and test models as an aid to understanding their experiments. An important complement to this project would be a database containing models, images, and biochemical and eletrophysiological data; such a database would not only support the Virtual Cell, but would also, independently, be an invaluable resource for the cell biology community. This proposal aims at investigating the feasibility of developing a database that can support the Virtual Cell. We will attempt to build a database that includes sets of equations that describe biochemical and electrophysiological reactions, cell geometry derived from microscopic images and spatial relationships amount the compartments of a cell. During this feasibility study, our data gathering will focus mostly on the data that are already available from our own laboratories. In addition, we will attempt to compile, group, and store a limited set of published reaction kinetics, eletrophysiological data, images and models into the database. Overall, our research focus associated with the database construction will be to study feasibility of organizing diversified sets of heterogeneous computational data so that the data can be seamlessly integrated into production and evaluation of computation models demonstrating complex cell biochemistry processes. The impact of the Virtual Cell Project is to revolutionize the way cell biologists study complex functions and behaviors of a living organism. A successful implementation of our feasibility study will allow us to produce a longer-term research framework. The longer-term research framework, once successful, will allow scientists to observe and examine detailed steps of chemical and kinematic changes without performing an actual experiment. We anticipate that such a resource would be very useful in both the laboratory and the classroom.