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Installation

Follow the uninstall instructions for your version of GeneMapper® Software. Before attempting to reinstall, verify that you are logged in locally as the Administrator, that your antivirus software is either off or that you have suspended activity during installation, and that your TCP/IP is installed.

Before uninstalling, make sure you have your GeneMapper® CD/DVD and your registration code for reinstallation. Follow the uninstall instructions for your version of GeneMapper® Software. Before attempting to reinstall, verify that you are logged in locally as the Administrator, that your antivirus Software is either off or that you have suspended activity during installation, and that your TCP/IP is installed.

If you received the error message about insufficient user privileges to start low level driver, you are most likely not logged in locally as the Administrator. Reboot the computer, change the domain to the local computer, and log in as the Administrator.

Right-click on Computer and select Properties. In the System section, look at the System Type and see if you have Windows® 7 Professional, 32-bit or 64-bit edition. Write this down, as you will need this information during the install process.

To install the necessary driver:

  1. Open a browser and go to https://www.ilok.com/#!home.
  2. On the right-hand side of the page, you should see the “Free Download License Support” links. If your computer has Windows® 7 Professional, 32-bit edition, select the middle option (“Windows 32-bit XP, Vista, 7, 8”). If your computer has Windows® 7 Professional, 64-bit edition, choose the third option (“Windows 64-bit XP, Vista, 7, 8”).

Note: If your browser gives you the choice to Run or Save, save the file. For the Internet Explorer® browser, you can choose the location to save the file. For Mozilla Firefox® and Google Chrome® browsers, the default location to save the file is the Downloads folder. 3. Run the installer. When the installation is complete, reboot the computer.

You should now be able to install the GeneMapper® Software 5 Demo.

Right-click on Computer and select Properties. In the System section, look at the System Type and see if you have Windows® 7 Professional, 32-bit or 64-bit edition. Write this down, as you will need this information during the install process.

To install the necessary driver:

  1. Open a browser and go to https://www.ilok.com/#!home.
  2. On the right-hand side of the page, you should see the “Free Download License Support” links. If your computer has Windows® 7 Professional, 32-bit edition, select the middle option (“Windows 32-bit XP, Vista, 7, 8”). If your computer has Windows® 7 Professional, 64-bit edition, choose the third option (“Windows 64-bit XP, Vista, 7, 8”).

Note: If your browser gives you the choice to Run or Save, save the file. For the Internet Explorer® browser, you can choose the location to save the file. For Mozilla Firefox® and Google Chrome® browsers, the default location to save the file is the Downloads folder.

   3. Run the installer. When the installation is complete, reboot the computer.

You should now be able to install the GeneMapper® Software 5 Demo.

Please download this PDF (GeneMapper® v.4.0 Uninstall– client install) and follow the steps listed to uninstall GeneMapper® Software v.4.0 from your stand-alone computer.

Please download this PDF (GeneMapper® v.4.0 uninstall) – full install and follow the steps listed to uninstall GeneMapper® Software v.4.0.

Please download this PDF (GeneMapper® v.4.1 Uninstall – client install) and follow the directions to uninstall GeneMapper® Software v.4.1.

Please download this PDF (GeneMapper® v.4.1 Uninstall Procedure – full install) and follow the directions to uninstall GeneMapper® Software v.4.1.

Please download this PDF (GeneMapper® 5 Uninstall – client install) and follow the directions to uninstall GeneMapper® Software 5.

Please download this PDF (GeneMapper® 5 Uninstall – full install) and follow the directions to uninstall GeneMapper® Software 5.

Please download this PDF for directions on how to resolve this error. 

Please download this PDF for directions on how to resolve this error. 

Please download this PDF for directions on how to resolve this error. 

Backing Up Data

It is useful to back up data in order to protect yourself from data loss, clearing out the Oracle® database to keep it from filling up, and/or for sending data to Technical Support for troubleshooting.

In GeneMapper® Software, there are 3 locations where you will need to back up data:

  1. Panel Manager – contains information on your Panels, Markers, and Bins.
  2. GeneMapper Manager – contains information pertaining to the Project itself – Projects, Analysis Methods, Size Standard Definitions, Table Settings, Plot Settings, Matrices (ABI PRISM® 310 Genetic Analyzer Only), Cluster Plot Settings, SNP Sets, and Report Settings.
  3. Data Files – sample data (.fsa files) that were used in the Project.

Note: Older versions of GeneMapper® Software contained an Archive function that would back up the entire database at once. However, the archive could only be reimported into the same instance of GeneMapper® Software. If you had a problem that required reinstallation of GeneMapper® Software, it would be considered a new instance of the software and the Archive could not be imported into it.

Follow the steps outlined below to export Kits, Panels, Markers, and Bin Sets found in Panel Manager:

  1. Open GeneMapper® Software and go to Tools Panel Manager.
  1. To export all Kits (top-level folders), Panels (sub folders), Markers, and Bin Sets all at once, highlight the word Panel Manager in the Navigator view on the left side. Go to File Export all Kits.



  2. When the display comes up, browse to the location where you would like to save your files and select Export All Kits. Only the name for the first panel will appear in the File name window, but all of the files will be backed up to the chosen location.



  3. When the files are saved, 1–2 files should be saved per kit. The first will have <Kit Name>_Panels.txt with the Panel and Marker information. If there is a Bin Set associated with the Panel, then a second file will be there with <Kit Name>_bins.txt.

    For backing up individual Panels or Bin Sets, click on the Kit (top-level folder) that contains the Panels and Markers you wish to back up. The File menu will now activate the options to Export Panels and Export Bin Sets.

  4. Save the text files to storage media (CD, DVD, network drive, thumb drive). If the GeneMapper® Software needs to be reinstalled or if you wish to put the information on another system, you can go to File Import Panels and Import Bin Sets to reimport the data.

To export project information, follow the steps outlined below:

  1. Go to the Tools menu and select GeneMapper® Manager.
  2. Click on the tab that contains the file(s) you want to back up or export.
  3. Select the file(s) that you want to export. Once they are selected, click on Export at the bottom of the window. (Projects can be selected by group, but the Save display will come up for each selected Project. In all of the other tabs, the files need to be exported one at a time).
  4. Browse to the location where you want to save the files and click on Export to save it.
  5. Save the files to the storage media of your choice (CD, DVD, network drive, flash drive). If the GeneMapper® Software needs to be reinstalled or if you wish to put the information on another system, you can go to the GeneMapper Manager, select the tab into which you wish to import, click on Import and import the files. Once the files are saved, you can delete any old files or projects to conserve or free up space in the database.

When a GeneMapper Project is created, the sample files are not imported into GeneMapper® Software, the location of the sample files is mapped within the project and edits are done to the project, leaving the raw data intact. This means that backing up a project will not also back up the files associated with the project. They will have to be backed up separately and reassociated to the project again if they are moved or if the software is reinstalled.

The location of the sample files will either be in the Runs folder (D:/AppliedBio/310/Runs) on the ABI PRISM® 310 Genetic Analyzer system or it will be determined by the Results Group in the Data Collection Software on the multi-capillary platforms. If you do not know where that location is, you can go to the Data Collection Software for your instrument and go to the Results Group section (top left corner in Unified Data Collection; for 3500 Data Collection, go to Library and in the Manage section, select Results Group), open the Results Group, and check the Sample File Folder location.

Save the files to the storage media of your choice (CD, DVD, network drive, flash drive). If you are moving projects to a new system or reinstalling GeneMapper® Software because of a hard drive failure, then you can move the sample files to the new location or new drive. When you open the project in GeneMapper® Software, go to FileàAssociate Samples and browse to the folder containing the samples for the project.

See the associated GeneMapper® Files, exported File Type, and data contained in each file below:

File

Exported
File Type

Data Contained in File

Projects

.ser

Sample file list, project settings, changes made to the project

Analysis Methods

.xml

Analysis Settings and filters information

Table Settings

.xml

What columns will be visible in the Samples and Genotypes table, font and size, and how it is sorted

Plot Settings

.xml

Plot View Preferences. Appearance of tables in Sample plot and Genotypes plot, Sizing table, labels and Display Settings

Cluster Plot Settings

.xml

Cluster Plot Preferences. SNP Table, Genotypes Cluster Plot table, and Display Settings for the Cluster Plot

Matrices

.mtx

Matrix file for the ABI PRISM® 310 Genetic Analyzer. Export to Matrix folder in the Data Collection Software

Size Standards

.xml

Color of the standard and peak size (bp) information for peaks that will be called

SNP Sets

.xml

SNPlex only. Information based on submitted SNP Pools

Report Settings

.xml

Customize what information you want to appear on the analysis report

Panels

.txt

Kit, Panel, and Marker information (color, range, name, etc.)

Bin Sets

.txt

Bins associated with the Panels, specific Location of peaks within the marker range

For Importing Data, you may want to start with the Panel Manager (Panels, Bin Sets) and then the GeneMapper Manager (Projects, Analysis Methods, etc.).

  1. Open the GeneMapper® Software and go to Tools Panel Manager.
  2. To import the Kits (top-level folders), Panels (subfolders), and Markers, select Panel Manager in the Navigator view on the left side.
  3. Go to File Import Panels.




  4. Select the Panel you want to import and click on Import. Note: Panels can only be imported one at a time via this method.


    This will import your Kits, Panels, and Markers. Once they are imported, click on the Kit (top-level folder) that contains the Panels and Markers to which you wish to associate the Bin Set. The File menu will now activate the options to Import Bin Set.



  5. Go to File→Import Bin Set, select the Bin Set you want to import, and click on Import.
  6. Once the Panels and Bins have been imported, click on Apply, then OK. Failure to hit Apply first may result in undoing the changes you have made.
  1. Go to the Tools menu and select GeneMapper Manager.
  1. Click on the tab for the file(s) you want to import.



  2. Click on Import at the bottom of the window and select the files to be imported. Note: Multiple projects can be selected for importing at one time, but all other tabs are one at a time.




    Once imported, the new files will appear in the list. When finished, click Done in the lower right corner.

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