Keizer, Ron J
UCSF / Pirana Software & Consulting BV
Objectives: Develop a “lite” version of Pirana for use on the UNIX command-line.
Background: Graphical user interfaces (GUIs) for NONMEM and PsN like Pirana[1], provide a convenient and powerful tool to perform modeling & simulation (M&S). However, the use of GUIs may be impeded for various reasons:
– when working on a remote cluster and only simple tasks are involved, it may be faster or more convenient to work from the command line (through ssh).
– more experienced modelers often prefer to work from the command line
– no GUI is currently available for mobile platforms (iOS / Android) to perform M&S on clusters
To address the points above, development of a command line-based interface to NONMEM and PsN was initiated (“cPirana”).
Methods: cPirana was written in Perl, using the NCurses::UI [2] module (which builds upon the ncurses library for user-interfaces on the UNIX command line). Where possible, routines previously developed for Pirana were re-used. For the layout of the interface, the “orthodox file manager”-style such as in Norton Commander[3] was chosen. cPirana was developed and debugged on linux and OSX. It was evaluated whether all functionality worked over remote ssh connections as well as locally, and whether cPirana could be used effectively from iOS devices (iPad, using the ssh-app “Prompt” to connect to a cluster over ssh).
Results: The Curses::UI library provided a stable GUI, and most of Pirana’s core functionality could be re-used with only minor code changes. Limited testing showed that cPirana provides a faster alternative to Pirana when working over slow cluster connections. Through ssh connections, all functionality could be accessed from iPad as well. Compared to Pirana, cPirana is less feature-rich, however the aim of this tool is different and there is no intention to implement all Pirana features in cPirana.
Conclusions: cPirana provides a comprehensive interface to NONMEM and PsN on the UNIX command line, allowing fast and easy access to core M&S tools. It also allows M&S on clusters from mobile devices.
References:
[1] Keizer RJ et al. Comput Methods Programs Biomed. 2011
[2] http://search.cpan.org/~mdxi/Curses-UI-0.9609/lib/Curses/UI.pm
[3] http://en.wikipedia.org/wiki/Norton_Commander
Reference: PAGE 22 (2013) Abstr 2806 [www.page-meeting.org/?abstract=2806]
Poster: New Modelling Approaches