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  76 <div class="style1" align="right">Welcome</div>
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  80 <div align="justify">
  81 <h3 class="heading1">Latest News</h3>
  82 <p>
  83
  84 Version 2.2.5 is available <a href="http://sourceforge.net/project/showfiles.php?group_id=101419">here</a>.</p>
  85
  86 <p>New features introduced in 2.2.5</p>
  87
  88 <p>- Monte Carlo Simulations (mcs) tool has been renamed to Stochastic
  89    Simulation and Estimation (sse), and has a bunch of new
  90    features. More information can be found in the SSE user guide
  91    distributed with PsN.</p>
  92
  93 <p>- Numerical Predictive Check (npc) and Visual Predictive Check
  94    (vpc) have been added to the toolbox. More information can be found
  95    in the NPC/VPC user guide distributed with PsN.</p>
  96
  97 <p>- Much improved results handling. Intermediate results are printed
  98    each time a NONMEM run has finished. A positive side effect is much
  99    reduced memory usage over all and in particular when running with
 100    many threads.</p>
 101
 102 <p>- Added support for G95. A more generic way of configuring compilers
 103    is on the way.</p>
 104
 105 <p>- 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).</p>
 106
 107
 108 <p>New features introduced in 2.2.4</p>
 109 <p>- Simulated data suitable for creating mirror plots can be generated
 110    by using a new options called --mirror_plots. The option takes a
 111    value which defines the number of simulations that will be
 112    generated.</p>
 113 <p>- A new option, --iofv, enables the computation of individual
 114    objective function values. These values are printed to a table file
 115    called iotab*, where * is the same number as is defined for any
 116    sdtab or patab tables. These names correspond to the normal Xpose
 117    table file format. If no sdtab or patab table is found in the
 118    NONMEM control stream, the iotab file is given number 1. </p>
 119 <p>- A brand new user command <tt>update_inits</tt> that will put
 120    final estimates from a NONMEM output file and put into a given
 121    model file. This is quite experimental. PsN will reformat the model
 122    file quite a lot and comments in the file might get lost. Your model
 123    file will be copied with the addition of a ".org" extension, so you
 124    wont lose your model.</p>
 125 <p>- "--compute_cwres" option renamed to simply "--cwres"</p>
 126
 127 <p>Bug Fixes  </p>
 128 <p>
 129
 130 - As usual, bugs were found and fixed between 2.2.4 and 2.2.5. Please
 131 read the
 132
 133 <a href="http://sourceforge.net/project/shownotes.php?group_id=101419&release_id=601480">
 134
 135 change logs</a>. These are also available in the README.txt file
 136 included in the release packege as usual. The most important bug fix
 137 is the removal of a memory leak in the results handling.
 138
 139 </p>
 140
 141
 142 <p><span class="heading1">Perl-speaks-NONMEM</span></p>
 143 <p>Perl-speaks-NONMEM (PsN) is a collection of Perl modules and programs aiding in the development
 144   of non-linear mixed effect models using NONMEM. The functionality ranges from solutions to simpler
 145   tasks such as parameter estimate extraction from output files, data file sub setting  and resampling,
 146   to advanced computer-intensive statistical methods. PsN includes stand-alone tools for the end-user
 147   as well as development libraries for method developers.
 148 </p>
 149 <p>
 150   Compared to previous versions of PsN 2, the ongoing work on PsN version 2.2 has brought some changes
 151   to the overall structure. PsN is now logically divided into three parts. Note, however, that you still
 152   only download and install one package.
 153 </p>
 154 <p>
 155 Most of what was included in the 2.0 release of PsN is now included in <b>PsN-Core</b>. PsN-Core is built around NONMEM's model, data and output
 156 files.  Through PsN-Core
 157 all parts of these files can be controlled in user-written Perl code. </p>
 158 <p>
 159 Using the functionality of PsN-Core we have implemented two new components: <strong>PsN-Toolkit</strong> and <strong>PsN-Utilities</strong>.</p>
 160 <p><strong>PsN-Toolkit</strong> is a collection
 161   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
 162   knowledge of Perl and some understanding of the toolkit framework. </p>
 163 <p><b>PsN-Utilities</b> is a set of command line programs
 164 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
 165 runs.
 166 </p>
 167 <p>You can read more about the different parts under <a href="docs.php">Documentation</a>.</p>
 168
 169 <p>
 170 Perl-speaks-NONMEM is copyright &copy; 2008 by Mats Karlsson, Niclas
 171 Jonsson and Andrew Hooker.<br>
 172 &copy;2006-2007 by Lars Lindbom.<br>
 173 &copy;2000-2005 by Lars Lindbom and Niclas Jonsson.<br>
 174 All rights reserved.
 175
 176 </p>
 177 <p>
 178 PsN is developed and maintained by <a href="mailto:pontus.pihlgren@farmbio.uu.se">Pontus
 179 Pihlgren</a> and <a href="mailto:kajsa.harling@farmbio.uu.se">Kajsa Harling</a>.
 180 </p>
 181
 182 <p>PsN was originally developed by Niclas Jonsson and continued by Lars
 183 Lindbom for his doctoral thesis.</p>
 184 <p>Additional implementation done by Jakob Ribbing, Kristin Karlsson,
 185 Maria Kjellsson, Joakim Nyberg and Andrew Hooker.</p>
 186 <p>Additional contributions by Radojka Savic, Paul Baverel, Martin Bergstrand, Elodie Plan and many more.</p>
 187
 188 <p>The site is designed and implemented
 189 by <a href="mailto:justin.wilkins@farmbio.uu.se">Justin
 190 Wilkins</a>.
 191 </p>
 192 <p>
 193 Perl-speaks-NONMEM is licensed under version 2 of the GNU General
 194 Public License as published by the Free Software Foundation.
 195 </p>
 196 <h3 class="heading1">References</h3>
 197 <ul>
 198     <li class="reference"> <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=
 199 16023764&query_hl=1&itool=pubmed_docsum">Lindbom L, Pihlgren P, Jonsson EN.</a> <br>
 200                 PsN-Toolkit--a collection of computer intensive statistical methods for non-linear mixed effect modeling using NON
 201 MEM. <br>
 202                 Comput Methods Programs Biomed. 2005 Sep;79(3):241-57. </li>
 203     <li class="reference"> <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=
 204 15212851&query_hl=1&itool=pubmed_docsum">Lindbom L, Ribbing J, Jonsson EN. </a> <br>
 205                 Perl-speaks-NONMEM (PsN)--a Perl module for NONMEM related programming.<br>
 206         Comput Methods Programs Biomed. 2004 Aug;75(2):85-94.</li>
 207 </ul>
 208
 209   <h3 class="heading1">Acknowledgments</h3>
 210 <p>
 211 NONMEM&reg; is a registered trademark of GloboMax. The Perl camel
 212 logo is a registered trademark of O'Reilly Media, Inc. and is used with
 213 permission. All logos and trademarks in this site are property of
 214 their respective owners.
 215 </p>
 216
 217 <p>
 218
 219 Thanks to Jeroen Elassaiss and Stefan Verhoeven for fixing bugs in SGE
 220 submission code.
 221
 222 </p>
 223
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