National Resource for Cell Analysis and Modeling

国家细胞分析和建模资源

• 批准号: 7300376
• 负责人: LESLIE M LOEW
• 金额: $ 106.56万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-09-30 至 2012-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7300376
• 关键词: National; Resource; Cell; Analysis; Modeling

DESCRIPTION (provided by applicant): Virtual Cell (VCell) is a problem solving environment, built on a central database, for analysis, modeling and simulation of cell biological processes. VCell integrates a growing range of molecular mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology, and can associate these with geometries derived from experimental microscope images. The National Resource for Cell Analysis and Modeling (NRCAM) has as its mission the growth of the VCell technology via research at the interface of physics, mathematics, computer science and biology. NRCAM is housed in a research center comprising an interdisciplinary faculty and containing state of the art facilities for studying living cells. This environment assures that experiment and theory drive each other synergistically. The technology research of this application is divided into 4 projects. Biophysical Mechanisms extends VCell into the domains of macromolecular aggregation, cytoskeletal dynamics and spatial electrophysiology, each of which can be treated in only a limited way with the current VCell. Numerical Tools will develop stiff solvers, adaptive meshing and parallelization to improve the efficiency and increase the size and complexity of spatial simulations; this project will also develop an elliptic solver to extend VCell simulations to biomechanics, spatial electrophysiology and steady state analysis. Enabling Technologies proposes to revise VCell by adopting a plugin architecture and augmenting the abstract software layers with a new multiphysics layer; these will effectively manage the complexity of the overall system to accommodate rapid application development. The Application Development project is charged with implementing enhancements for VCell through both internal development (e.g. grid computing, stand-alone VCellApps and visualization tools) and adoption of an open software development model that will encourage external contributions. Thirteen collaborative projects designed to drive the VCell development with investigators from around the US are described. Through training, dissemination and collaborative activities, NRCAM promotes a quantitative approach to cell biological research. VCell represents an advanced tool for investigations of the cellular basis of disease, especially as related to the cardiac, nervous and immune systems and cancer. As the database of models expands, simulating drug actions and side effects will become increasingly feasible.

描述（由申请人提供）：虚拟细胞（VCELL）是一个解决问题的环境，构建在中央数据库上，用于分析，建模和模拟细胞生物学过程。 VCELL整合了越来越多的分子机制，包括反应动力学，扩散，流动，膜转运，侧膜扩散和电生理学，并可以将它们与从实验显微镜图像中得出的几何形状相关联。国家细胞分析和建模资源（NRCAM）通过在物理，数学，计算机科学和生物学的界面上进行研究，将VCELL技术的发展作为其使命。 NRCAM位于一个研究中心中，该研究中心包括一个跨学科的教职员工，并包含研究活细胞的最先进的设施。这种环境确保实验和理论相互协同驱动。该应用程序的技术研究分为4个项目。生物物理机制将VCELL扩展到大分子聚集，细胞骨架动力学和空间电生理学的结构域，每种都可以用当前VCELL以有限的方式对其进行处理。数值工具将开发僵硬的求解器，自适应网格和并行化，以提高效率并提高空间模拟的大小和复杂性；该项目还将开发一个椭圆求解器，以将VCELL模拟扩展到生物力学，空间电生理学和稳态分析。启用技术建议通过采用插件体系结构并使用新的多物理层增强抽象软件层来修改VCELL；这些将有效地管理整个系统的复杂性，以适应快速的应用程序开发。该应用程序开发项目负责通过内部开发（例如网格计算，独立VCELLAPP和可视化工具）实施VCELL的增强，并采用开放软件开发模型，以鼓励外部贡献。描述了13个旨在推动来自美国各地的调查人员来推动VCELL开发的合作项目。通过培训，传播和协作活动，NRCAM促进了细胞生物学研究的定量方法。 VCELL代表了研究疾病细胞基础的先进工具，尤其是与心脏，神经和免疫系统和癌症有关的工具。随着模型数据库的扩展，模拟药物作用和副作用将变得越来越可行。