Pirana is a modeling workbench for RsNLME, NONMEM, and PsN, offering a graphical user interface and many auxiliary tools to support modeling and simulation analyses. It can be used for modeling on a local system or on computer clusters. Pirana can be used to run, manage, and edit models, interpret output, and manage NONMEM installations. It is easily extendable with custom scripts, and integrates smoothly with R, Xpose4, Excel and other software.
Model management is enhanced through descriptions, notes, and coloring of models and results lists. Pirana provides condensed and detailed model information displays, as well as both list and tree views. Pirana offers wizards and templates to aid in model creation, duplicates models with updated run- and table numbers and parameter estimates, and will delete model files and all associated results and table files.
In terms of results management, Pirana creates HTML and LaTeX run reports that are formatted and contain basic model specifications and estimations results for all estimation methods that were used, including parameter estimates, uncertainty, shrinkage etc. Custom R-scripts can be used from within Pirana and run on a specific model, e.g., to automate creation of goodness-of-fit plots and automatically load the output. Pirana comes with multiple useful scripts, ready for customization. Pirana’s Data Inspector allows detailed investigation of, e.g., goodness-of-fit plots, or plots of covariates against individual parameter estimates. Pirana’s main window provides an overview of dataset files, output files, Xpose4 files, and R scripts. The data files and Xpose4 datasets can be opened and edited with a spreadsheet, code editor, or in R. Notes can be added to datasets. Pirana also has tools for converting between NONMEM table files and CSV format and converting $DES code to Berkeley Madonna or R-deSolve code for simulation purposes.
Pirana offers tools for local and cluster NONMEM installation management. NONMEM run progression can be monitored. Pirana also reads intermediate NONMEM output and provides numerical and graphical view of parameters and gradients
Execution of models using PsN is available through Pirana’s PsN dialog, which accepts all PsN commands and allows selection of the NONMEM version to use. The actual command line that is used is displayed and can be edited. The dialog also shows all PsN information for the specific command. Pirana also contains a wizard for creating an scm configuration file.
Pirana supports clusters and has wizards for the creation of configuration files for NONMEM parallel computation features. Computer clusters running NONMEM can be accessed directly through SSH, both from/to Linux and Windows systems. Pirana can be installed on the cluster server and run by multiple clients through SSH-X-window tunneling.
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