PMx Software
This site provides access to the PMx software for analysis and management of pedigreed populations.
The
manual is ready! It is included in the current installation, and can also be
downloaded here.
Our thanks to Kathy Traylor-Holzer for editing the manual, and to her and a wonderful group of colleagues for writing the sections of the manual. We expect to revise the manual regularly, and new versions will be included in new PMx installations and upgrades.
The most recent version of PMx is version 1.0.20120322.
PMx is most easily used as an accessory program to the SPARKS software or
the PopLink software for studbook management.
SPARKS has been developed by ISIS (International
Species Information System). To use SPARKS as the studbook management
software to prepare files for PMx, you should have the latest upgrade to Sparks
(version 1.63) or at least be using Sparks 1.56. The upgrade for Sparks is
available at http://www.vortex9.org/sparks16.html.
The current version is Sparks 1.63 (19
Feb 2012), and it has had some significant enhancements that improve its data
exports to PMx.
PopLink has been developed by Lincoln Park Zoo and can be downloaded from www.lpzoo.org/poplink.
PMx can also be used as a stand-alone program for population management, if the
demographic and genetic data are first prepared in a specific format.
See the PMx manual for more information.
A paper in Methods in Ecology and Evolution presenting an overview of PMx is available at http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00148.x/pdf.
PMx
was developed by:
- Jonathan Ballou, National Zoological Park
- Robert Lacy, Chicago Zoological Society
- JP Pollak, Cornell University
- with help from many friends.
Development
of PMx was supported by:
- National
Zoological Park
- Chicago Zoological Society
- Institute for Museum and Library Services
The
concepts and design of PMx benefitted immensely from input by the AZA Small Population
Management Advisory Group, the EAZA European Population Management Advisory
Group, the International Species Information System, and colleagues in zoos and
conservation organizations around the world.
Cautions
PMx is distributed free of charge. It is provided without any promise of support. The primary developers of PMx and a large number of collaborating colleagues have attempted to provide the best, most current methods and tools to assist with the management of pedigreed populations. PMx is distributed with no guarantee that the methods perform as intended or described, that the computer code is without bugs that could influence results, or that the program is suitable for any particular purpose.
PMx
is copyrighted, but is distributed without cost for the purpose of furthering
conservation and research. Individuals and not-for-profit organizations are
hereby given licenses for using PMx in research, teaching, animal management,
and conservation.
Distribution of PMx is restricted to:
- distribution by the Chicago Zoological Society;
- distribution by the National Zoological Park;
- distribution by IUCN SSC Conservation Breeding
Specialist Group;
- distribution by the International Species Information
System as an accessory program for use with licensed copies of their
software;
- distribution by the World Association of Zoos and
Aquariums (WAZA), or any of its any of the member associations;
- downloading of the program from this web site by
individuals and not-for-profit organizations for their own teaching,
research, and conservation applications;
- redistribution without charge of the
unmodified installation program for the purposes described above.
To
download the full installation of the latest version of PMx
go to http://www.vortex9.org/PMx/PMxInstallation.msi
If
your system settings block you from downloading an msi
file, you can try instead to download http://www.vortex9.org/PMx/PMxInstallation.zip,
from which the msi installation file can be unzipped
(extracted).
To
download update files for replacing program files of a prior version of PMx go
to http://www.vortex9.org/PMx/PMxUpdate.zip.
However,
if the updated files do not work for you, you may need to do the full
installation again.
The
PMx manual can be downloaded from www.vortex9.org/PMx/PMxManual.pdf.
To
download the latest upgrade of Sparks go to http://www.vortex9.org/sparks16.html.
The current version is 1.63, release date 19 February 2012.
Bug
fixes and significant enhancements:
8 May 2011
- Fixed lack of updating of Pairwise
tab when Selection was changed.
- Now allows change to more of the Individual variables
(on the Individual tab). However, be careful! Changes to an Individual’s
values can impact results, are not easily reversible, and do not change
any data in the original studbook.
- Some improvements made to Age Distribution graph and
Demography Custom graphs.
- Few fixes made to SPARKS 1.6 (fixed file now on the
above link).
9 May 2011
- Fixed an error in how Potential Retention was displayed
for founders with UNK parents.
22 July 2011
- A handful of cosmetic bugs were fixed, and a few new
features (e.g., Seasonality tests) were added to Demography.
4 September 2011
·
Changes
were made to the default folders for importing data and saving projects.
·
Fixes
were made to the way that kinships and MateRx MSI
values were calculated and displayed if a population has no known ancestry but
the user requested to treat UNK parents as (at least partly) WILD.
·
Improvements
were made in the information displayed in the Project Notes shows import file
filters and other information.
13 October 2011
- A number of changes were made to enable changes to MateRx settings, fix an error in the %known
calculations for some populations, and otherwise.
1 November 2011
- A bug was fixed that could prevent dead animals from
being included in Genetic History tables and graphs.
10 November 2011
- Previously, not all Genetic Assumptions were saved when
a project was saved and then re-opened. Now they should be.
5 December 2011
·
A
test was added to alert the user if an individual is its own ancestor.
28 December 2011
·
A
change was made to the default folder where sample files are installed. (It is
now C:\PMxProjects\Samples.) It is recommended that your PMxProjects
be placed either in this folder or in some other folder created on the C:
drive, because on some Windows systems user files cannot be placed within the
program folder. The PMx program is still installed in the ProgramFiles
folder on the user’s computer, but this can be changed (for example, to C:\
PMx) during the installation.
14 January 2012
·
An
option was added to Genetics Settings to read a UDF file after the project is
created.
·
AutoCull can now be specified to select only from the filtered cull
table.
·
An
option was added to AutoCull to cull until the GD
cannot be improved with further culls.
·
An
individual variable was added that displays a list of all descendants of an
individual.
·
Some
improvements were made to the display of lists on the Selection screen, as you
toggle between Genetic and Demographic selections.
15 January 2012
·
The
newly created manual has been added to the installation and included as the
Help system of the program.
18 January 2012
·
A
handful of relatively minor fixes were made to deal with certain kinds of
problematic data, improved translations to Japanese and Spanish, and displaying
some variables with more precision.
2 February 2012
·
Some
enhancements and bug fixes were made in the Demography section. Genetics was
changed to allow negative kinships and inbreeding coefficients to be entered in
an empirical kinship matrix. An option was added to the Selection tab to allow
adding of new individuals that were not in the original imported pedigree file.
14 February 2012
·
A
new version of Sparks (1.63) is now available.
27 February 2012
·
The
ability to create new animals at the Selection tab was added.
·
Better
documentation of input files in the Project Notes, and the ability to export
Project Notes, was added.
·
Changes
made to the Model Life Tables are now saved with the project.
1March 2012
·
A
few fixes were made to the filtering of tables, especially for those who use
languages other than English.
·
Changes
were also made to how the Recommendations table is saved and reloaded, and this
too will mostly affect users that are not using the English version.
9 March 2012
·
A
fix was made to the import of files created by PopLink.
·
A
fix was made to the saving and re-loading of BirthType
data.
22March 2012
·
A
button to access further details about Management Sets, including founder
statistics, was added.
·
Some
changes were made to make the reading/writing of kinship matrices more
efficient.
Other cosmetic or minor
adjustments have been made from time to time.
Redistribution
of PMx, in whole or in part, by any for-profit organization or for any
profit-making purposes is expressly forbidden.
Changes last made on: 22 March 2012