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首页> 外文期刊>Computer Methods and Programs in Biomedicine: An International Journal Devoted to the Development, Implementation and Exchange of Computing Methodology and Software Systems in Biomedical Research and Medical Practice >Pirana and PCluster: a modeling environment and cluster infrastructure for NONMEM.
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Pirana and PCluster: a modeling environment and cluster infrastructure for NONMEM.

机译：Pirana和PCluster：NONMEM的建模环境和集群基础结构。

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摘要

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.
机译：使用非线性混合效应模型（NONMEM）进行药代动力学-药效学建模是一项功能强大且具有挑战性的技术，因为通常可以从命令行访问该软件。开发了图形用户界面Pirana，它为NONMEM提供了完整的建模环境，使新手和高级用户都可以提高工作流程的效率。 Pirana提供了以下功能：管理和创建模型文件，概述建模结果，创建运行报告以及处理数据集和输出表，以及在模型输出上运行自定义R脚本。通过安全外壳（SSH）协议，Pirana也可以用于连接到Linux群集（SGE，MOSIX）以分配工作负载。使用NONMEM进行建模会增加计算负担，可以通过将运行分配给计算机群集来减轻这种负担。这里提供了一个解决此问题的方法，称为PCluster。该平台易于设置，可以在标准网络环境中运行，并且可以根据需要通过其他节点进行扩展。该集群支持Perl讲的NONMEM（PsN）建模工具包，并且可以包括专用或非专用PC。使用Perl编写的守护程序脚本旨在在后台在集群中的每个节点上运行，并管理作业分配。可以从Pirana访问PCluster，并且两种软件产品都已在大型学术网络上进行了广泛的测试。该软件在开放源代码许可下可用。

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