Piraña: Open source modeling environment for NONMEM
Ron J Keizer, JG Coen van Hasselt, Alwin DR Huitema
Dept. of Pharmacy and Pharmacology, The Netherlands Cancer Institute / Slotervaart Hospital
Introduction
Piraña is a modeling environment for NONMEM, and provides an easy-to-use toolkit for both novice and advanced modelers. It can be used for modeling on a local system or on computer clusters, and provides interfaces to NONMEM, PsN and Wings for NONMEM. Piraña can be used to run, manage and edit models, interpret output, and manage NONMEM installations. It is easily extendible with custom scripts, and integrates smoothly with R, Xpose, Excel and other software. Piraña fully supports NONMEM version 7 and runs on Windows, Linux and Mac OSX.
Model management
- Logbook-like interface for model management
Add descriptions, notes, and coloring to models and results. Choose between condensed / detailed model information, and list / tree views. - Create and edit models
Create new models from templates, duplicate model with updated run- and table numbers and parameter estimates. Delete model files and all associated results and table files.
Results management
- Create HTML / LaTeX run reports
Quickly create formatted reports for a run, containing basic model specifications and estimations results for all estimation methods that were used, including parameter estimates, uncertainty, shrinkage etc. Piraña is compatible with output from NONMEM version 5, 6 and 7. - Extend Piraña with custom scripts
Custom scripts (R / Perl / Awk / Python) can be used conveniently from within Piraña and run on a specific model, e.g. to automate creation of goodness-of-fit plots. The output image / PDF / html-file can be loaded automatically. Multiple useful scripts are already included with Piraña, which can be customized. - Built-in Data Inspector
Allows detailed investigation of e.g. goodness-of-fit plots, or plots of covariates against individual parameter estimates. - Overview of datasets, output, Xpose files, R scripts
Quickly open, edit data files and Xpose datasets with a spreadsheet, code editor or in R. Make notes to datasets. - Convert NONMEM table files to CSV format and vice-versa.
- Multiple other functionality included
NONMEM, PsN and WFN
- Install and manage local / cluster NONMEM installations
Install NONMEM 5, 6, or 7 from Piraña, or add existing installation to be used in Piraña. Manage and view SIZES variables for NM6 and NM7 installations. - Run a selected model in the current folder or in a separate folder. Conveniently choose the desired NONMEM installation from a list.
- Follow NONMEM run progression
Piraña reads intermediate NONMEM output and provides numerical and graphical view of parameters and gradients - Start model execution using the PsN dialog
All PsN commands can be used from a dialog window. The NONMEM version used by PsN for the command can be chosen from a list. The actual command line that is used is displayed and can be edited. The dialog also shows all PsN information for the specific command. - Run models using Wings for NONMEM, using NMGO or NMBS
Cluster support
- Connect to computer clusters through SSH
Computer clusters running NONMEM can be accessed directly through SSH, both from/to Linux and Windows systems. - Piraña can be installed on the cluster server, and run by multiple clients through SSH-X-window tunneling
- Simple cluster set-up under Windows networks [1]
This feature allows the construction of a simple cluster using dedicated or non-dedicated PCs, e.g. desktop PCs from co-workers. This may be specifically interesting for small modeling groups.
Software
Piraña is written in Perl/Tk and released under an open-source license (GNU/GPL). It runs on Windows, Linux, and Mac OSX. The current version is 2.3.0, which can be downloaded from http://pirana.sf.net. Future development may include: more advanced QA functionality, support for S-ADAPT / WinBUGS / Monolix, or a Piraña iPhone / Android App, but depends on time and needs of the developers.
References
[1] Keizer RJ, Zandvliet AS, Huitema ADR. A simple infrastructure and graphicaluser interface (GUI) for distributed NONMEM analysis on standard network environments. PAGE 17 (2008) Abstr 1237
