MCELL SIMULATIONS OF NEURAL MODELS USING APST

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 为了分析脑组织的微观结构，研究人员正在 使用蒙特卡罗模拟。其中最成功的是Mcell，一位将军 Tom Bartol和Tom Bartol开发的细胞微生理学蒙特卡罗模拟器 乔尔·斯泰尔斯在康奈尔大学时(与埃德·萨尔彼特，以及 已故的米里亚姆·萨尔彼特)。巴托尔和斯泰尔斯现在在索尔克研究所， 匹兹堡超级计算中心。 Mcell生成高真实感的亚细胞结构的3D模拟 生理学，允许神经信号的未知方面 进行了定量建模。与加州大学圣地亚哥分校(UCSD)的合作伙伴和 田纳西大学，这项研究的参与者 Alpha项目在提供支持网格的 Mcell的版本，可以处理比Mcell更大、更逼真的数据集 以前是有可能的。 Mcell的研究人员一直受到缺乏足够的计算能力的限制 基础设施以及使用它来适应大规模模拟的能力 以及导航和映射大的参数空间。关键限制因素 包括高效访问 远程计算、存储和联合数据库资源，能够 计划应用程序以利用不断变化的可交付资源 性能，以及管理分布式和异类资源的能力 在统一的、面向服务的框架内。Mcell代表一种 一大类NPACI元系统应用程序，现在可以通过NPACKage 利用NPACI和其他网格资源进行大规模运行--这是一项壮举 以前只有相当困难才能完成。 Mcell的使用有三种典型场景： 在典型工作站或小型工作站集群上的小规模使用。 元计算环境中的大规模参数扫描使用。这是 使用带有APST的Mcell完成。 在大规模并行超级计算机上的单个大规模模拟 蓝色地平线。这是通过将Mcell与海带一起使用实现的，称为Mcell-K。 APST是一个网格应用程序执行环境，它自动执行 调度和部署“参数扫描”应用程序，即 由大型独立计算任务集组成的应用程序，具有 潜在的大型数据集。Mcell就属于这类应用程序。阿普斯特 连接到多个中间件基础设施以启动和监控 在各种网格资源上进行计算，以便在网格之间移动数据 存储资源，并收集有关网格状态的信息 站台。APST使用复杂的调度算法，考虑到 调度计算时数据移动的成本。 APST为Mcell用户提供对本地和NPACI资源的透明访问， 在很大程度上保护用户不受大量身份验证的影响， 要遇到的存储和排队系统。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In order to analyze the microscopic structure of brain tissue, researchers are using Monte Carlo simulations. One of the most successful is MCell, a general Monte Carlo simulator of cellular microphysiology developed by Tom Bartol and Joel Stiles when they were at Cornell University (with Ed Salpeter, and the late Miriam Salpeter). Bartol and Stiles are now at the Salk Institute and the Pittsburgh Supercomputing Center, respectively. MCell produces highly realistic 3-D simulations of subcellular architecture and physiology, allowing unexplored aspects of neural signaling to be quantitatively modeled. Together with partners at UC San Diego (UCSD) and the University of Tennessee, participants in this alpha project have made significant progress toward providing a grid-enabled version of MCell that can handle much larger, more realistic data sets than previously possible. MCell researchers have been limited by the lack of adequate computational infrastructure and the ability to use it to accommodate large-scale simulations as well as to navigate and map large parameter spaces. Key limiting factors include the ability to efficiently access remote computational, storage, and federated database resources, the ability to schedule the application so as to exploit fluctuating deliverable resource performance, and the ability to manage distributed and heterogeneous resources within a unified, service-oriented framework. MCell is representative of a large class of NPACI metasystem applications which, through NPACKage, can now leverage NPACI and other Grid resources for large runs -- a feat which previously could only be accomplished with considerable difficulty. There are three typical scenarios for use of MCell: Small scale usage on typical workstations or small clusters of workstations. Large-scale parameter sweep usage in a metacomputing environment. This is accomplished using MCell with APST. Single large-scale simulations on massively parallel supercomputers such as BlueHorizon. This is accomplished using MCell with KeLP, called MCell-K. APST is a Grid application execution environment that performs automatic scheduling and deployment of "parameter sweep" applications, that is applications consisting of large sets of independent computational tasks with potentially large datasets. MCell belongs to this class of applications. APST interfaces to several middleware infrastructures to launch and monitor computation on a wide variety of Grid resources, to move data among Grid storage resources, and to gather information about the status of the Grid platform. APST uses sophisticated scheduling algorithms that take into account the cost of data movements when scheduling computation. APST provides MCell users with transparent access to local and NPACI resources, shielding the user, to a large degree, from the vast array of authentication, storage, and queuing systems to be encountered.