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

项目摘要 虚拟单元（VCell）是一个建立在中央数据库上的问题解决环境， 作为客户端-服务器应用程序传播。它的设计是为了让数学上复杂的 细胞生物学家可以使用的计算建模和模拟。资源是开放的， 免费提供给细胞生物学和科学软件开发者社区。目前有 >6300名用户通过VCell服务器构建模型并运行模拟，所有用户均保存在 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、侧向膜扩散、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分析或实验图像的几何形状。用户可能 在多种可用的模拟方法中选择：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， 空间混合随机/确定性模拟。新开发的 技术现在允许在几何形状中模拟反应扩散方程， 改变形状开发现有VCell技术所需的研究已经展开 在20年的时间里。这项拨款申请的目的是保持大的可用性， VCell平台提供的大量数据和独特功能， 社区它还将提供时间来计划一个谨慎和深思熟虑的过渡到一个自我- VCell资源的持续财务模型。

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.