The Virtual Cell: a Computational Resource for Collaborative Modeling and Simulation of Cell Biology

虚拟细胞：细胞生物学协作建模和仿真的计算资源

• 批准号: 9810875
• 负责人: LESLIE M LOEW
• 金额: $ 52.83万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9810875
• 关键词: 20 year old; 3-Dimensional; Aging; Algorithms; Applications Grants; Binding; Biological Process; Biomedical Technology; Biophysical Process; Cardiology; Cell model; Cell physiology; Cells; Cellular biology; Client; Communities; Community Developments; Computer Simulation; Computer software; Custom; Data; Databases; Development; Diabetes Mellitus; Differential Equation; Diffusion; Disease; Electrophysiology (science); Equation; Foundations; Geometry; Goals; Grant; Hybrids; Image; Imagery; Improve Access; Individual; Infrastructure; Institutes; Institution; Investments; Kidney Diseases; Kinetics; Lateral; Longevity; Malignant Neoplasms; Mathematics; Membrane; Methods; Modeling; National Institute of General Medical Sciences; Online Systems; Policies; Problem Solving; Reaction; Recovery; Reproducibility; Research; Resources; Running; Science; Services; Shapes; Software Engineering; Software Tools; Source; Supporting Cell; Technology; Time; Transmembrane Transport; United States National Institutes of Health; Wisconsin; base; built environment; central database; computing resources; cost; design; experimental study; insight; live cell imaging; live cell microscopy; mathematical model; models and simulation; nervous system disorder; new technology; open source; outreach; particle; portability; preservation; repository; scientific computing; simulation; software development; tool; user-friendly; virtual

Project Summary Virtual Cell (VCell) is a problem solving environment built on a central database and disseminated as a client-server application. It is designed to make mathematically sophisticated computational modeling and simulation accessible to cell biologists. The resource is open and free to the cell biology and scientific software developer communities. Currently, there are >6300 users who have built models and run simulations through the VCell servers, all saved in the VCell database. VCell supports a number of key biophysical mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion, electrophysiology and rule-based models of multi-state/multi-molecular interactions. Reaction-diffusion simulations can be based on 1D, 2D or 3D analytical or experimental image-based geometries. Users may choose among multiple available simulation approaches: ordinary differential equations, partial differential equations, stochastic reaction kinetics, network-free simulations, spatial particle- based simulations and spatial hybrid stochastic/deterministic simulations. A newly developed technology now allows for simulations of reaction diffusion equations in geometries with changing shape. The research needed to develop the existing VCell technology was developed over a period of 20 years. This grant application aims to preserve the availability of the large amount of data and unique functionality provided by the VCell platform for the scientific community. It will also provide the time to plan for a careful and deliberate transition to a self- sustaining financial model for the VCell resource.

项目摘要 虚拟单元（VCELL）是基于中央数据库的问题解决环境， 作为客户服务器应用程序传播。它旨在使数学上的复杂 细胞生物学家可以访问的计算建模和仿真。资源开放， 免费提供细胞生物学和科学软件开发人员社区。目前，有 > 6300个用户通过VCELL服务器构建了模型并运行模拟，全部保存在 VCELL数据库。 VCELL支持许多关键的生物物理机制，包括反应 动力学，扩散，流动，膜转运，外侧膜扩散，电生理学和 基于规则的多状态/多分子相互作用的模型。反应扩散模拟可以 基于1D，2D或3D分析或基于图像的几何形状。用户可以 在多种可用的仿真方法中选择：普通微分方程，部分 微分方程，随机反应动力学，无网络模拟，空间粒子 - 基于模拟和空间混合随机/确定性模拟。一个新开发 现在，技术允许模拟与几何形状中的反应扩散方程 变化形状。开发现有VCELL技术所需的研究是开发的 在20年的时间内。该赠款申请旨在保留大型的可用性 VCELL平台为科学提供的数据和独特功能 社区。它还将提供时间计划仔细，刻意过渡到自我的时间 维持VCELL资源的财务模型。