Pirana and PCluster: A modeling environment and cluster infrastructure for NONMEM
Pirana and PCluster: A modeling environment and cluster infrastructure for NONMEM
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DOI：
10.1016/j.cmpb.2010.04.018
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发表时间：
2011-01-01
影响因子：
6.1
通讯作者：
Huitema, Alwin D. R.
中科院分区：
文献类型：
--
作者：
Keizer, Ron J.;van Benten, Michel;Huitema, Alwin D. R.
使用非线性混合效应建模(NONMEM)的药代动力学-药效学建模是一种功能强大但具有挑战性的技术，因为该软件通常从命令行访问。开发了一个图形用户界面Pirana，它为NONMEM提供了一个完整的建模环境，使新手和高级用户都能够提高他们的工作流程的效率。Pirana提供了用于管理和创建模型文件、概述建模结果、创建运行报告、处理数据集和输出表以及在模型输出上运行定制R脚本的功能。通过安全外壳(SSH)协议，Pirana还可以连接到Linux集群(SGE，MOSIX)以分配工作负载。使用NONMEM建模计算繁琐，可以通过将运行分配到计算机集群来缓解。这里提供了一个解决此问题的方案，称为PCluster。该平台易于设置，可在标准网络环境中运行，并可在需要时添加额外的节点进行扩展。该集群支持建模工具包Perl Speech NONMEM(PSN)，并且可以包括专用或非专用PC。用Perl编写的守护程序脚本被设计为在集群中的每个节点的后台运行，并管理作业分发。PCluster可以从Pirana访问，这两种软件产品都在一个大型学术网络上进行了广泛的测试。该软件是在开放源码许可证下提供的。(C)2011爱思唯尔爱尔兰有限公司。保留所有权利。
Pharmacokinetic-pharmacodynamic modeling using non-linear mixed effects modeling (NONMEM) is a powerful yet challenging technique, as the software is generally accessed from the command line. A graphical user interface, Pirana, was developed that offers a complete modeling environment for NONMEM, enabling both novice and advanced users to increase efficiency of their workflow. Pirana provides features for the management and creation of model files, the overview of modeling results, creation of run reports and handling of datasets and output tables, and the running of custom R scripts on model output. Through the secure shell (SSH) protocol, Pirana can also be used to connect to Linux clusters (SGE, MOSIX) for distribution of workload.Modeling with NONMEM is computationally burdensome, which may be alleviated by distributing runs to computer clusters. A solution to this problem is offered here, called PCluster. This platform is easy to set up, runs in standard network environments, and can be extended with additional nodes if needed. The cluster supports the modeling toolkit Perl speaks NONMEM (PsN), and can include dedicated or non-dedicated PCs. A daemon script, written in Perl, was designed to run in the background on each node in the cluster, and to manage job distribution. The PCluster can be accessed from Pirana, and both software products have extensively been tested on a large academic network. The software is available under an open-source license. (C) 2011 Elsevier Ireland Ltd. All rights reserved.