MCELL SIMULATIONS OF NEURAL MODELS USING APST

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目及 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 为了分析脑组织的微观结构，研究人员在 使用蒙特卡罗模拟。 其中最成功的是麦克赛尔， 由Tom Bartol开发的细胞微生理学蒙特卡罗模拟器， 乔尔斯泰尔斯当他们在康奈尔大学（与艾德萨尔彼得，和 已故的米里亚姆·萨尔彼得）。 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产生高度逼真的亚细胞结构的三维模拟， 生理学，允许神经信号的未探索方面， 定量建模。 与加州大学圣地亚哥分校（UCSD）和 田纳西大学，参与者 alpha项目在提供支持网格的 MCell版本，可以处理更大，更真实的数据集， 以前可能的。 MCell研究人员一直受到缺乏足够计算能力的限制， 基础设施和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 包括有效访问 远程计算、存储和联合数据库资源， 调度应用程序，以便利用波动的可交付资源 性能，以及管理分布式和异构资源的能力 在一个统一的、面向服务的框架内。 MCell是一种 NPACI元系统应用程序的大类，通过NPACKage，现在可以 利用NPACI和其他网格资源进行大规模运行--这是一项壮举， 以前只能通过相当大的困难来实现。 MCell有三种典型的使用场景： 在典型工作站或小型工作站集群上的小规模使用。 元计算环境中大规模参数扫描的使用。 这是 使用MCell和APST完成。 在大规模并行超级计算机上进行单个大规模模拟， 蓝色地平线 这是使用MCell和KeLP完成的，称为MCell-K。 APST是一个网格应用程序执行环境， 调度和部署"参数扫描"应用程序，即 由大量独立计算任务组成的应用程序， 潜在的大数据集。 MCell就属于这类应用。 APST 连接到多个中间件基础架构，以启动和监控 在各种各样的网格资源上进行计算，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 平台 APST使用复杂的调度算法， 调度计算时的数据移动成本。 APST为MCell用户提供对本地和NPACI资源的透明访问， 在很大程度上屏蔽了用户，使其免受大量的身份验证， 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.