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.

项目概要 Virtual Cell (VCell) 是一个建立在中央数据库和 作为客户端-服务器应用程序进行传播。它的目的是使数学复杂 细胞生物学家可以使用计算建模和模拟。资源是开放的并且 免费提供给细胞生物学和科学软件开发者社区。目前，有 >6300 个通过 VCell 服务器构建模型并运行模拟的用户，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、膜传输、侧膜扩散、电生理学和 基于规则的多状态/多分子相互作用模型。反应扩散模拟可以 基于 1D、2D 或 3D 分析或实验图像几何结构。用户可以 在多种可用的模拟方法中进行选择：常微分方程、偏微分方程 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。一种新开发的 技术现在允许模拟反应扩散方程的几何形状 改变形状。开发现有 VCell 技术所需的研究已完成 超过20年的时间。该赠款申请旨在保留大量资金的可用性 VCell 平台为科学领域提供的数据量和独特功能 社区。它还将提供时间来计划仔细而深思熟虑地过渡到自我管理。 VCell 资源的维持财务模型。