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Latest News

Version 2.2.5 is available here.

New features introduced in 2.2.5

- Monte Carlo Simulations (mcs) tool has been renamed to Stochastic Simulation and Estimation (sse), and has a bunch of new features. More information can be found in the SSE user guide distributed with PsN.

- Numerical Predictive Check (npc) and Visual Predictive Check (vpc) have been added to the toolbox. More information can be found in the NPC/VPC user guide distributed with PsN.

- Much improved results handling. Intermediate results are printed each time a NONMEM run has finished. A positive side effect is much reduced memory usage over all and in particular when running with many threads.

- Added support for G95. A more generic way of configuring compilers is on the way.

- When running on SGE PsN will name the job after the modelfile that is being run, previously the jobs were not explicitly named and SGE just reported them as "perl" (Thanks to Darin Perusich for this feature).

New features introduced in 2.2.4

- Simulated data suitable for creating mirror plots can be generated by using a new options called --mirror_plots. The option takes a value which defines the number of simulations that will be generated.

- A new option, --iofv, enables the computation of individual objective function values. These values are printed to a table file called iotab*, where * is the same number as is defined for any sdtab or patab tables. These names correspond to the normal Xpose table file format. If no sdtab or patab table is found in the NONMEM control stream, the iotab file is given number 1.

- A brand new user command update_inits that will put final estimates from a NONMEM output file and put into a given model file. This is quite experimental. PsN will reformat the model file quite a lot and comments in the file might get lost. Your model file will be copied with the addition of a ".org" extension, so you wont lose your model.

- "--compute_cwres" option renamed to simply "--cwres"

Bug Fixes

- As usual, bugs were found and fixed between 2.2.4 and 2.2.5. Please read the change logs. These are also available in the README.txt file included in the release packege as usual. The most important bug fix is the removal of a memory leak in the results handling.

Perl-speaks-NONMEM

Perl-speaks-NONMEM (PsN) is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM. The functionality ranges from solutions to simpler tasks such as parameter estimate extraction from output files, data file sub setting and resampling, to advanced computer-intensive statistical methods. PsN includes stand-alone tools for the end-user as well as development libraries for method developers.

Compared to previous versions of PsN 2, the ongoing work on PsN version 2.2 has brought some changes to the overall structure. PsN is now logically divided into three parts. Note, however, that you still only download and install one package.

Most of what was included in the 2.0 release of PsN is now included in PsN-Core. PsN-Core is built around NONMEM's model, data and output files. Through PsN-Core all parts of these files can be controlled in user-written Perl code.

Using the functionality of PsN-Core we have implemented two new components: PsN-Toolkit and PsN-Utilities.

PsN-Toolkit is a collection of computer intensive statistical methods for non-linear mixed effect modeling using NONMEM. The toolkit includes Perl modules for Bootstrapping, Jackknifing, Log-likelihood Profiling, Case-deletion Diagnostics and Stepwise Covariate Model building. Using a module from PsN-Toolkit requires some basic knowledge of Perl and some understanding of the toolkit framework.

PsN-Utilities is a set of command line programs that allows the user to use the functionality of PsN-Core and PsN-Toolkit without the need to write Perl code. Apart from programs for all the tools in PsN-Toolkit, PsN-Utilities includes utilities that perform simpler tasks, such as summarizing the output from NONMEM runs.

You can read more about the different parts under Documentation.

PsN is developed and maintained by Pontus Pihlgren and Kajsa Harling.

PsN was originally developed by Niclas Jonsson and continued by Lars Lindbom for his doctoral thesis.

Additional implementation done by Jakob Ribbing, Kristin Karlsson, Maria Kjellsson, Joakim Nyberg and Andrew Hooker.

Additional contributions by Radojka Savic, Paul Baverel, Martin Bergstrand, Elodie Plan and many more.

The site is designed and implemented by Justin Wilkins.

Perl-speaks-NONMEM is licensed under version 2 of the GNU General Public License as published by the Free Software Foundation.

References

Lindbom L, Pihlgren P, Jonsson EN.
PsN-Toolkit--a collection of computer intensive statistical methods for non-linear mixed effect modeling using NON MEM.
Comput Methods Programs Biomed. 2005 Sep;79(3):241-57.
Lindbom L, Ribbing J, Jonsson EN.
Perl-speaks-NONMEM (PsN)--a Perl module for NONMEM related programming.
Comput Methods Programs Biomed. 2004 Aug;75(2):85-94.

Acknowledgments

NONMEM® is a registered trademark of GloboMax. The Perl camel logo is a registered trademark of O'Reilly Media, Inc. and is used with permission. All logos and trademarks in this site are property of their respective owners.

Thanks to Jeroen Elassaiss and Stefan Verhoeven for fixing bugs in SGE submission code.

PsN is hosted at SourceForge.