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

Version 2.3.1 was released December 16, 2008.

Changes between PsN 2.3.1 and 2.3.2

1. Added support for censored and categorical data in vpc.
   Please see the updated userguide for details.

2. Added some simple error checking in $OMEGA and $SIGMA parsing.

3. Enabled negation of some common options (e.g. -compress).

4. 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.

5. Fixed a bug to the sse that caused options not to be passed correctly.

6. Fixed a bug to sumo that prevented the user from setting some options.

7. Fixed a bug in the code for running on Torque (the torgue bug).

8. Replaced the computational principles of nonpb version 1.

9. Fixed a bug in the input checking of vpc/npc.

Changes between PsN 2.3.0 and 2.3.1

1. Updated the sse_userguide.

2. Added support for models with block SIGMA structure in NONMEM VI
   2.0.

3. Fixed a bug to the bootstrap that caused options not to be passed
   correctly

4. Added support for the Torque grid computing system.

5. Fixed a bug so that the -mplots flag works with bootstrap and llp.

Changes between PsN 2.2.5 and 2.3.0

1. Support for NONMEM VI 2.0 has been added.

2. Major documentation effort. All command-line help texts have been
   reviewed and updated.

3. 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.

4. 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.

5. Changed principle for selecting best result from a set of retries.
   Please see the change log or the README.txt file for details.

6. 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"

7. New script called "psn_options" that lists options common to most scripts ("psn_options -h").
   

8. New version of sumo, including help texts. see "sumo -help"

9. Lots of new additions and changes, please see the change log or the README.txt file for details.
   

More information

Perl-speaks-NONMEM is copyright
©2008 by Mats Karlsson, Niclas Jonsson and Andrew Hooker.
©2006-2007 by Lars Lindbom.
©2000-2005 by Lars Lindbom and Niclas Jonsson.
All rights reserved.

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 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 and implemented by Justin Wilkins. It is now maintained by Andrew Hooker.

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.