Virtual Cell modelling and simulation software environment.
Virtual Cell modelling and simulation software environment.
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DOI：
10.1049/iet-syb:20080102
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发表时间：
2008-09
影响因子：
2.3
通讯作者：
Loew LM
中科院分区：
文献类型：
--
作者：
Moraru II;Schaff JC;Slepchenko BM;Blinov ML;Morgan F;Lakshminarayana A;Gao F;Li Y;Loew LM
虚拟细胞（VCell; http://vcell.org/）是一个解决问题的环境，建立在一个中央数据库上，用于分析、建模和模拟细胞生物过程。VCell集成了越来越多的分子机制，包括反应动力学、扩散、流动、膜运输、侧膜扩散和电生理学，并可以将这些与实验显微镜图像得出的几何形状联系起来。它是作为基于web的分布式客户机-服务器系统开发和部署的，在全球拥有一千多名用户。VCell提供了层（核心技术和抽象）的分离，表示生物模型、物理机制、几何、数学模型和数值方法。这种分离澄清了建模决策、假设和近似的影响。其结果是物理上一致，数学上严谨，空间建模和仿真框架。用户创建生物模型，VCell将自动(i)生成运行模拟所需的适当数学编码，（ii）生成并编译适当的计算机代码。支持确定性和随机算法来描述和运行非空间模拟；使用有限体积数值算法的完整偏微分方程求解器可用于复杂细胞几何形状的反应-扩散-平流模拟，包括从显微镜图像导出的3D几何形状。使用VCell数据库，模型和模型组件可以被重用和更新，也可以在协作组之间私下共享，或者发布。通过导入/导出SBML、CellML和MatLab格式，可以与其他工具交换模型。此外，用于组件唯一标识的外部数据库绑定机制和符合MIRIAM标准的标准化注释促进了模型的管理。VCell现在是开源的，它的原生模型编码语言（VCML）是一个公共规范，它代表了使用基于插件的新平台的新一代更定制的、以实验为中心的建模工具的基础。
The Virtual Cell (VCell; http://vcell.org/) 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. It has been developed and deployed as a web-based, distributed, client-server system, with more than a thousand world-wide users. VCell provides a separation of layers (core technologies and abstractions) representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. This separation clarifies the impact of modeling decisions, assumptions, and approximations. The result is a physically consistent, mathematically rigorous, spatial modeling and simulation framework. Users create biological models and VCell will automatically (i) generate the appropriate mathematical encoding for running a simulation, and (ii) generate and compile the appropriate computer code. Both deterministic and stochastic algorithms are supported for describing and running non-spatial simulations; a full partial differential equation solver using the finite volume numerical algorithm is available for reaction-diffusion-advection simulations in complex cell geometries including 3D geometries derived from microscope images. Using the VCell database, models and model components can be reused and updated, as well as privately shared among collaborating groups, or published. Exchange of models with other tools is possible via import/export of SBML, CellML, and MatLab formats. Furthermore, curation of models is facilitated by external database binding mechanisms for unique identification of components and by standardized annotations compliant with the MIRIAM standard. VCell is now open source, with its native model encoding language (VCML) being a public specification, which stands as the basis for a new generation of more customized, experiment-centric modeling tools using a new plug-in based platform.
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影响因子：
46.9
作者：
Le Novère, N;Finney, A;Wanner, BL
通讯作者：
Wanner, BL
影响因子：
4.4
作者：
Salis, H;Kaznessis, Y
通讯作者：
Kaznessis, Y
DOI：
10.1126/stke.3442006re6
发表时间：
2006-07-18
期刊：
Science's STKE : signal transduction knowledge environment
影响因子：
--
作者：
Hlavacek, William S;Faeder, James R;Fontana, Walter
通讯作者：
Fontana, Walter
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
DOI：
10.1016/j.pbiomolbio.2004.01.004
发表时间：
2004-06-01
影响因子：
3.8
作者：
Lloyd, CM;Halstead, MDB;Nielsen, PF
通讯作者：
Nielsen, PF