Piraña: The flexible modeling environment for NONMEM
J.G. Coen van Hasselt (1,3), Ron J. Keizer (2,3)
(1) Dept. of Pharmacy and Pharmacology, The Netherlands Cancer Institute / Slotervaart Hospital, the Netherlands. (2) Pharmacometrics Research Group, Uppsala University, Sweden. (3) Pirana Software & Consultancy.
Introduction
Piraña is a modeling environment for NONMEM and PsN, 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. 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, Xpose4, Excel and other software. Piraña fully supports NONMEM version 7.2 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 wizard and 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 , 7.2. - Extend Piraña with custom scripts
Custom R-scripts 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.
- Convert $DES code to Berkeley Madonna or R-deSolve code for simulation purposes.
- Multiple other functionalityincluded
NONMEM
- 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
PsN
- 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. - Special functionality for scm: create configuration file using wizard, select scm file from run dialog.
- Support for PsN run record syntax
Cluster support
- Wizards for creation of configuration files for parallel computation features of NM7.2.
- 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.
Software
Piraña is written in Perl/Tk and released under a Create Commons license for academic use, and a commercial license. Supported operating systems include Windows, Linux, and Mac OSX. The current version is 2.4.0, which can be downloaded from http://www.pirana-software.com/.
References
[1] Keizer et al. Piraña and PCluster: A modeling environment and cluster infrastructure for NONMEM. J Comp Meth Progr Biomed (2011). 101 (1), 1.
