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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. You can read more about the different parts of PsN under Documentation.

Latest news

Version 3.0.0 was released October 2, 2009 , and is available here.

Version 2.3.2 was released June 24, 2009 , and is available here.

Version 2.3.1 was released December 16, 2008.

New features in PsN 3.0.0

NONMEM7 support for NONMEM6 type input
PsN 3.0.0 has partial support for NONMEM7. It will handle NONMEM6 type input, i.e. single $ESTIMATION and classical estimation methods, with any PsN tool (bootstrap, scm...). PsN 3.0.0 has full support for NONMEM6. Details in release notes.
New option nmfe:
There is a new commandline option -nmfe (no arguments) that can be used with any PsN tool. When enabled, PsN will invoke nmfe6 or nmfe7 to run NONMEM instead of doing stepwise compiling and execution. See psn_configuration.pdf and common_options_defaults_version.pdf for details. When nmfe is set the compiler configuration is ignored.
Compiler configuration The compiler configuration can be set differently for each NONMEM version. See psn_configuration.pdf for details.

Minor changes and bug fixes in PsN 3.0.0

Fixed the -clean option and documentation so that the behaviour matches the documentation.
Fixed a bug that caused bootstrap to crash when dataset has no header.
The psn.mod file in NM_run subdirectory is now the selected model from the set of retries, instead of the last model that was run.
Fixed a bug to -iofv option for NONMEM6 on Windows. (-iofv is not supported for NONMEM7 since iofv values are obtained from phi additional output.)
Removed old experimental database code.
Added a temporary solution to file path problem on windows and old perl5.8 build versions. Thanks to Joachim Grevel.
Fixed a bug to rewriting model compartments (line break at wrong place).
Added handling of commas in comments to parameters using a solution provided by Bill Denney and Jeroen Elassaiss-Schaap.
Changed sge queueing of jobs. Awaiting test result from Justin Wilkins who reported the bug.
Changed npc/vpc to use CWRES in $TABLE if NONMEM7 is used , and to allow longer variable names.
Changed installer script setup.pl so that it no longer installs required perl modules, but instead optionally checks if required modules are installed.
Changed installer script so that documentation is copied to doc subdirectory of PsN installation directory.
Updated error messages to give more information.

New documentation in PsN 3.0.0

Installation instructions are found in psn_installation.pdf.
In psn_configuration.pdf it is described how to edit psn.conf to configure PsN correctly. Please read that document before running PsN for the first time. Old psn.conf files must be edited to work correctly with PsN3.
The document known_bugs_and_workarounds.pdf lists the most commonly encountered unfixed bugs and how to work around them.

Click here to show older change notes

Changes between PsN 2.3.1 and 2.3.2

Added support for censored and categorical data in vpc.
Please see the updated userguide for details.
Added some simple error checking in $OMEGA and $SIGMA parsing.
Enabled negation of some common options (e.g. -compress).
Changed the default value of option -restarts from 5 to 0
in the source code. Please note: Users can set their own
defaults in psn.conf, see instructions here.
Fixed a bug to the sse that caused options not to be passed correctly.
Fixed a bug to sumo that prevented the user from setting some options.
Fixed a bug in the code for running on Torque (the torgue bug).
Replaced the computational principles of nonpb version 1.
Fixed a bug in the input checking of vpc/npc.

Changes between PsN 2.3.0 and 2.3.1

Updated the sse_userguide.
Added support for models with block SIGMA structure in NONMEM VI
2.0.
Fixed a bug to the bootstrap that caused options not to be passed
correctly
Added support for the Torque grid computing system.
Fixed a bug so that the -mplots flag works with bootstrap and llp.

Changes between PsN 2.2.5 and 2.3.0

Support for NONMEM VI 2.0 has been added.
Major documentation effort. All command-line help texts have been
reviewed and updated.
User-guide documents for common PsN options, bootstrap, execute,
sse, vpc, npc, llp and cdd are now available in the folder "doc"
under the PsN Core and Toolkit installation directory, which is
chosen during the installation (e.g. C:\Perl\site\lib\doc). There
are still gaps, but they are smaller than before.
New feature to help make runs more reproducible: A new file,
"version_and_option_info.txt" is created in the run directory
(<scriptname>_dirXX) whenever execute/sse/bootstrap/npc or any of
the other major PsN scripts are run. The file contains the PsN
version, the date and time, the actual values of the optional
options to the script, the command that started the run and the
actual values of optional general PsN options. The general PsN
options include nm_version (NONMEM version as named in psn.conf) and
seed.
Changed principle for selecting best result from a set of retries.
Please see the change log or the README.txt file for details.
New script called "psn" that lists all PsN scripts available using "psn -h" or "psn -help", and lists all available NONMEM versions (the ones listed in psn.conf) using "psn -nm_versions"
New script called "psn_options" that lists options common to most scripts ("psn_options -h").
New version of sumo, including help texts. see "sumo -help"
Lots of new additions and changes, please see the change log or the README.txt file for details.

More information

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

PsN is developed and maintained by Kajsa Harling, Sebastian Ueckert and Andrew Hooker.

PsN was originally developed by Niclas Jonsson and continued by Lars Lindbom for his doctoral thesis. Additional implementation has been done by Pontus Pihlgren, Jakob Ribbing, Kristin Karlsson, Maria Kjellsson and Joakim Nyberg. Additional contributions by Radojka Savic, Paul Baverel, Martin Bergstrand, Elodie Plan and many more.

This website was designed, implemented and is maintained by Sebastian Ueckert.

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.