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

虚拟细胞项目旨在开发一个框架，设计用于模拟细胞生物过程，其中包含数学，物理和数字作为透明的基础设施。该项目的成功实施将使细胞生物学家有可能构建和测试模型，以帮助理解他们的实验。这个项目的一个重要补充将是一个包含模型、图像、生化和电生理数据的数据库；这样的数据库不仅可以支持虚拟细胞，而且还可以独立地成为细胞生物学社区的宝贵资源。本提案旨在探讨开发一个支持虚拟单元的数据库的可行性。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方程集，从显微镜图像中得出的细胞几何形状以及细胞隔室的空间关系。在这项可行性研究中，我们的数据收集将主要集中在我们自己实验室已经获得的数据上。此外，我们将尝试汇编、分组和存储一组有限的已发表的反应动力学、电生理学数据、图像和模型到数据库中。总的来说，我们与数据库建设相关的研究重点将是研究组织各种异构计算数据集的可行性，以便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。虚拟细胞计划的影响是彻底改变细胞生物学家研究生物体复杂功能和行为的方式。可行性研究的成功实施将使我们能够制定一个长期的研究框架。长期研究框架，一旦成功，将允许科学家观察和检查化学和运动学变化的详细步骤，而无需进行实际的实验。我们期望这样的资源在实验室和课堂上都非常有用。

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.