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PLT Tools: A Graphical Interface for the NONMEM System

From: Dennis Fisher <fisher>
Date: Tue, 29 Sep 2009 06:40:07 -0700

Colleagues,

Steve Shafer and I are pleased to announce a major new release of PLT =

Tools, version 2.3, a Graphical Interface for the NONMEM System. PLT =

Tools now provides all the tools necessary to conduct and manage a
NONMEM analysis. In addition to NONMEM's normal operation, PLT Tools =

provides fully-automated support for visual predictive check,
bootstrap analysis, likelihood profile, and jackknife analysis.

Recent enhancements include:
Graphics: When an analysis is run for the first time, "data
checkout" graphics are created automatically.

Real-time Parameters: When NONMEM's estimation step in being run, a =

window displays the objective function and all THETAS graphically each =

time that the output file is updated.

Simultaneous NONMEM runs: Multi-core computers (most new computers =

have multiple processors or cores) can run simultaneous instances of
NONMEM, thereby improving throughput (requires a license)

Network access: Users with access to a network of computers on which =
 
NONMEM is installed can run NONMEM on multiple machines simultaneously =

(requires a license + a supplemental network fee) from a single
desktop computer.

Control stream library: A library of control streams is provided.

Control stream editor: The user can edit the control stream directly =
 
from the graphical editor. Alternatively, the user can access an
external editor directly from the graphical interface.

User-defined graphics: Users familiar with R/S-Plus code can
piggyback their own code to produce graphics for each NONMEM run.
Many of PLT Tools' functions are made available to the user, thereby
permitting these graphics to have the same format as graphics created =

by PLT Tools. If the user is not familiar with R/S-Plus and requires =

additional graphics, these can be provided through a consulting
arrangement.

Project Log: Every NONMEM run is entered into a log for that
project. Contents include the run timestamp, the $PROBLEM statement, =

the mode (e.g., FO vs. FOCE), objective function, number of digits
attained, and whether standard errors were obtained. This log can be =

saved as a CSV file. The log enables the user to access graphics,
NONMEM outputs, and control streams from previous runs.

Parameter Log: For each NONMEM run, the objective function and all =

paramete estimates (THETAS, OMEGAS, SIGMAS) are entered into a log for =

that project. This log is saved as a CSV file.

Automation: The user can assemble a list of control streams to run =

(templates are provided), then PLT Tools will run each of these in
sequence. This is particularly useful if an entire project needs to
be re-run because of minor changes in the data.

Installer: An installer assures seamless installation.

For those of you not acquainted with PLT Tools, PLT Tools facilitates =

conduct of NONMEM analyses on either the Windows, Linux, or OS X
platforms. PLT Tools is a suite of tools that includes the following:

Project Controller: Using a graphical interface, run NONMEM, then =

automatically create numerous files containing NONMEM outputs and
tables, create extensive graphics, and perform various statistical
analyses. Folders are created automatically, all source documents are =

archived, and all files are time-stamped, facilitating Part 11
compliance. Tables created by NONMEM are copied, then reformatted so =

that they open automatically in Excel. A unique feature is a 1-2 page =

summary ("Brief Summary") showing the objective function, the number
of significant digits, final estimates for thetas (plus standard
errors if available), omegas, and sigmas and diagnostics of NONMEM
boundary conditions. Examples of these various files are available at =

PLTsoft.com.

Compare Runs: Compare one or more pairs of runs:
    change in the objective function
    P value for the likelihood ratio test
    line-by-line comparison of the two control streams.
The output is a text file that can be inserted as an appendix in a
study report. A separate comma-delimited table summarizes differences =

between runs, objective functions and the change between models, the P =

value for the likelihood ratio test, the number of non-fixed thetas,
etas, and sigmas in each model, and comments entered by the user.
Also, the "brief summaries" described above are bundled into a single =

document which can then be used an an appendix in a study report.

Create Archive: With one click, bundle together the outputs of
multiple runs into a time-stamped archive. Ideal for transfer or
archiving of a completed project.

These tools are facilitated by the following:

Graphics Editor: Using a graphical interface, select options for the =
 
creation of graphics. No knowledge of S-Plus/R code is required.

Run Listing Editor: During an analysis, timestamps for all runs are =

tabulated. Using pull-down menus, select the runs to be used by the
Compare Runs and Create Archive Tools.

PLT Tools is available via download from PLTsoft.com. The free version =

provides nearly all features (see the Licensing page on the website
for details). Licensing unlocks the remaining features. Installation =

is automatic (via an installer), provided that NONMEM 5, 6, or 7 is
already installed (PLT Tools is fully compatible with NONMEM 7). PLT =

Tools requires that NONMEM be installed with Globomax's installer
(which creates a file nmfe6 or nmfe6.bat [or nmfe7 or nmfe7.bat]); PLT =

Tools does not work with Wings for NONMEM (Holford) or nmqual (Metrum).

Details, examples, and downloads are available at PLTsoft.com.
Questions can be directed to info

Dennis Fisher

Dennis Fisher MD
P < (The "P Less Than" Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
Received on Tue Sep 29 2009 - 09:40:07 EDT

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