VIRTUAL CELL USER COMMUNITY

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 虚拟细胞是一种通用的建模工具，可以在互联网上免费获得，专门为实验生物学家设计。该软件允许用户使用简单的面向生物学的图形用户界面来制定复杂的生化反应途径，包括膜运输和电生理学。为了在虚拟细胞中模拟特定的路径和网络，首先按名称添加分子物种，然后使用简单的反应编辑器输入反应。然后，以这种方式产生的每个反应都被分配到细胞内适当的隔间，建立一个完整的途径。随后，隔室可以映射到均匀均匀区域的近似值(隔室模型)，或者映射到由解析表达式构建的几何图形，或者直接从研究中细胞的显微镜图像得出。对于模型中描述的每个特定交互，用户选择适当的动力学形式并输入相关参数值。然后由该软件自动生成表示该模型的数学方程系统。所有这些活动都是在用户的计算机上完成的，使用在会话开始时自动上传的基于Java的复杂用户界面，并将结果保存到UCHC服务器上的虚拟细胞数据库(VCDB)。然后，基于模型并结合特定实验条件的模拟使用可用的数值方法的选择来求解，这些方法使用来自我们的中央设施的硬件和软件资源(例如，高性能计算机集群、特定求解器、库和编译器)。模拟结果保存到高容量数据存储设备并链接到VCDB，并可以查看和导出为多种格式，可以使用现有的成像或电子表格软件进行加载和进一步分析。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The Virtual Cell is a general modeling tool, freely available over the Internet, designed specifically for experimental biologists. The software permits the user to formulate complex biochemical reaction pathways including membrane transport and electrophysiology with a simple biology-oriented graphical user interface. To model specific pathways and networks in the Virtual Cell, molecular species are first added by name, and reactions entered using a simple reaction editor. Each reaction created in this way is then assigned to the appropriate compartment within the cell, building a complete pathway. The compartments can subsequently be mapped to either an approximation of well-mixed uniform regions (compartmental model), or to geometries constructed from analytical expressions, or derived directly from microscope images of the cell under study. For each specific interaction described in the model, the user chooses the appropriate kinetic formalism and inputs relevant parameter values . A system of mathematical equations representing the model is then automatically generated by the software. All these activities are completed on the user's computer, using a sophisticated Java-based user interface uploaded automatically at the beginning of the session, and the results of it are saved to the Virtual Cell Database (VCDB) on UCHC servers. Simulations based on the model and incorporating specific experimental conditions are then solved using a choice of available numerical methods, which use hardware and software resources (e.g. highperformance clusters of computers, specific solvers, libraries, and compilers) from our central facility. Results of simulations are saved to a high-capacity data storage facility and linked into the VCDB, and can be viewed and exported to a number of formats that can be loaded and further analyzed with available imaging or spreadsheet software.