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 PMx FAQs

If you have a question about the use of PMx, please read the manual, then search the FAQs below, and then -- if you don't find an answer, submit your question.

 


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Q:>  I tried to download the new installation, but I got a warning about a bad or missing certificate (or unknown publisher). Also, when I did download it, it crashes when I run the new version with an error about missing files. What is wrong?  Submit Answer

      A:>  You can safely ignore that warning. We cannot afford the cost and hassle of becoming a "known" publisher (in MS's eyes), but no one has ever encountered a virus in our software. If you get errors when trying to run a new version (or if the installation fails for whatever reason), then first uninstall the old version, then download and install the newest version, and then reboot. The problem often is that Windows doesn't fully install and recognize all the new files in the installation unless you go through these steps.


Q:>  Problem running PMx on a computer with Japanese operating system?  Submit Answer

      A:>  PMx crash due to Japanese traditional calendar In Japanese operating systems, the date may be shown using the traditional Japanese calendar. For example, 2016 is Heisei 28 (see further explanation below). On a Japanese computer July 1, 2016 would be displayed as 28/07/01. This causes PMx all sorts of problems and it crashes. If you are having problems with PMx crashing on a Japanese computer, check the dates being used. You might have to change them back to the Western system for PMx to run. You can also check the version of PMx. It should be something like 1.3.YYYYMMDD. We originally noticed this problem when PMx crashed on Kanako’s computer and we also noticed that the PMx version was shown as 1.3.280601 (!). So Kanoko changed the setting of the date display to 2016/07/01, downloaded the installer, uninstalled and reinstalled PMx, then the error was fixed. For more information about the Japanese calendar: http://www.meijigakuin.ac.jp/~watson/ref/mtsh.html)


Q:>  How is Ne calculated in PMx?  Submit Answer

      A:>  Two ways: (1) Ne = (4 * MB * FB) / (MB + FB) Where MB are FB are the number of living male and female proven breeders in the population. Weighed by proportion known? (2) By measuring the loss of gene diversity over time in the population and calculating what size of Ne would have resulted in that loss according to the formula: GDt/GD0 = [1 – 1/(2Ne)]t Where GDt is the current gene diversity and GD0 is the initial gene diversity and t is the number of generations since the founders. Version (1) Ne is shown in PMx on page ………… Version (2) Ne is shown in PMx on page ………..


Q:>  I downloaded and installed the newest version, but now I can't open old projects and even building new projects just leads to an error message when I try to import data.  Submit Answer

      A:>  It sounds as though something did not get installed right when you uploaded the newest version. My suggestion would be that you go into Control Panel and uninstall PMx. Then download again the msi installation file from www.vortex10.org/PMx.aspx. Then run that installation again.


Q:>  How to do you find out the inbreeding co-efficient on PMX - I am stuck !  Submit Answer

      A:>  The inbreeding coefficient for each individual is given in one of the columns of data in the Individual tab within the Genetics section.


Q:>  I am unable to save my settings regarding customisation of tables - PMx shows 'Settings cannot be saved'. Also, on start-up PMx shows message 'Default data quality file missing' and asks to use factory settings. Any answers please?  Submit Answer

      A:>  The message about default settings can usually be safely ignored. PMx is just updating some settings to the most current version. Regarding the issue with customization of tables, can you send a Bug Report that gives the details?


Q:>  Suppose you had a population in which one birth was parthogenetic. How would that be dealt with in PMx? How do you set up the data to incorporate it?  Submit Answer

      A:>  It depends on what kind of parthenogenesis it was. If it was the equivalent of selfing – with the offspring formed by the fusion of two independent gametes – then you enter the DamGAN in the dam field and enter SELF for sire. I would expect that it would do the same thing to enter the DamGAN in both the dam and sire fields. (I don’t think that this form of parthenogenesis is very common in mammals or herps, but probably is seen, as is almost everything, in fishes and inverts.) If it was the equivalent of cloning – with the offspring being formed from a diploid cell from the dam – then you enter the Dam and enter CLONE for the sire code. I don’t think that this happens much, if ever, in mammals or birds, but it does happen in some parthenogenetic (and usually polyploid) lizard and salamander species. If the offspring was formed by a haploid gamete dividing and then the two identical haploid cells fusing (this usually occurs by the two products of the 2nd meiotic division fusing), so that the offspring is homozygous at all loci, then enter the dam and enter HAPLOID for the sire. I think that this is the most common kind of facultative parthenogenesis in reptiles (e.g., some snakes, komodo monitors, etc.).


Q:>  Where can I get help with the use of PMx?  Submit Answer

      A:>  The first place to look is the Manual. If that doesn't have the information that you need, you might be able to get help from the population management advisors for your regional zoo association. If that is not an option for you, submit your query to this FAQ section, and hope that someone can provide you with an answer. Good luck!


Q:>  What does it mean when I get an error message about a "forbidden" character in my data file?  Submit Answer

      A:>  PMx uses the '[' and ']' characters in a special way to mark certain kinds of data. Therefore, data (IDs, locations, etc.) cannot contain either of these characters. Remove them, and then everything should work OK.


Q:>  When I try to re-load my PMx project, I get an error message about "Index was out of range." What does that mean?  Submit Answer

      A:>  Unfortunately, it can mean almost anything. Somewhere in the reading or processing of your data, PMx encountered data that was not in a format that it could read. One possible cause of this is that you may have used a character within an animal ID, location, or UDF that has special meaning to PMx. Characters that PMx uses to separate fields (and therefore should be avoided within the data of any fields include: '[', ']', ‘|’, ‘;’, and ‘:’. Another possible reason that PMx could give that error message is that the pmxproj file was somehow corrupted. Save it as a backup somewhere and then try to re-create the project.


Q:>  Is there a pedigree drawing program that can work with PMx?  Submit Answer

      A:>  The program Lineage does a very nice job of displaying and allowing you to manipulate visualizations of pedigrees. Lineage was created by JP Pollak and Kevin Egan, and is available at jppollak.com. PMx automatically creates a .txt file (and places it into the .pmxproj zip file) that is of the format needed by Lineage. Note, however, that Lineage may not work correctly on computers with European data formats, in which the comma is the decimal delimiter.


Q:>  I got a notice that a new PMx is available, but when I download the installation, it still seems to be a version that is month's out of date. Is there something newer?  Submit Answer

      A:>  Yes, there is a new PMx (release date 14 June 2013) and the installation is on the website. The problem is that internet servers will often provide you with previously stored ("cached") versions of files unless you tell your browser to force the server to go to the website to get the latest version. Usually, you can do this by hitting F5 or the "refresh" icon on your browser after you go to the download website.
      A:>  Further info about this problem ... sometimes even hitting F5 won't successfully refresh a download link. A way to force any url to get a fresh copy rather than anything stored in memory is to add "?xx=9999" to the end of the url (without the quotes). E.g., to get the latest PMx you can go to www.vortex10.org/Downloads/PMxInstallation.msi?xx=9999


Q:>  I'm working on the Komodo dragon population and have a question about the best way to enter a parthenogenic parent into the studbook so that it is most accurately represented in PMx genetics. The AZA studbook records the dam as the actual dam and the sire as UNK. The EAZA studbook records both the dam and sire as the dam. Both are kind of close to being right, but either way the genetic analysis isn't completely accurate for either situation.  Submit Answer

      A:>  Recording the same animal as both SIRE and DAM will work in some cases, but different modes of parthenogenetic reproduction have different genetic consequences. How you tell PMx what was the form of reproduction depends on just what the animals did genetically, although the general approach for such cases of uniparental reproduction is to enter a special code in the SIRE field, and then enter the one parent in the DAM field. The available special codes are: CLONE – use this if the progeny are all identical genetic replicas of the dam. SELF – use this if the progeny were produced by a sexual mating of a hermaphroditic dam to herself (resulting in offspring that have inbreeding of F = 0.50). Note that I think this option will give you the same results as if you enter the same animal for SIRE and DAM. HAPLOID – use this if the progeny were either haploid (developed from unfertilized eggs) or produced from the fusion of two identical meiotic products (“diploid” but with the two sets of chromosomes being identical), resulting in offspring that are completely inbred. The few tests that have been done on the parthenogenetically produced Komodos (and a few other reptiles) showed that they resulted from the “Haploid” mechanism above. This is unfortunate, because it results in the poorest retention of genetic diversity, but it is better than no reproduction at all! You probably can’t enter “HAPLOID” as the sire in the studbook, so you will need to edit the export file to get this inserted correctly for PMx.


Q:>  Is the code for PMx available as open-source?  Submit Answer

      A:>  No. Although it might be great to have community development of PMx, the community of people with the expertise in both pedigree analysis and C# programming is too small to support an active open-source development of the tool. Moreover, the program is used globally for management of endangered populations, and the organizations using PMx need to know that there is quality control of the distributed version.


Q:>  Can PMx be used on a Mac?  Submit Answer

      A:>  PMx was developed for Windows-based PCs. It can run on a Mac that is running a version of Windows OS or a Windows emulator. The details of how to do this will need to be provided by some Mac-user. (Anyone want to offer further information?)
      A:>  PMx can be run on a Mac if you have a Virtual Windows machine running. I have been using Parallels Desktop on my MacBook with Windows XP for years and succesfully ran PM2000 and PMx on it. This should be possible with any Windows emulation software on the Mac. Just start up your virtual Windows machine, use the install files to and you're ready to go.

 


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