Frequently Asked Questions

The public BIONUMERICS Calculation Engine will remain operational until December 31st, 2024. After December 31st, 2024, the public BIONUMERICS Calculation Engine wil be discontinued and no updates or support will be provided. As such, the public BIONUMERICS Calculation Engine can thus no longer be used to perform analyses.   

BIONUMERICS 8 users can still use the local PC-based Calculation Engine after December 31st, 2024, with the restriction that new alleles cannot be submitted.

Credits will be sold until the end of 2023.  After that, you will have one year to use the purchased credits, as the public BIONUMERICS Calculation Engine will not be accessible after the end of 2024. 

The BIONUMERICS support website will be taken offline on December 31^st, 2024. From that moment on, support materials such as PDF tutorials and manuals will not be available anymore. We provide a bulk download for PDF tutorials and manuals from the two latest major software versions. All PDF manuals (i.e., the reference manual, all plugin manuals and the installation guide) can be downloaded as a single ZIP archive. Likewise, all PDF tutorials (organized by category) are available for download as a ZIP archive. Simply download and extract the archives that correspond to the software version you are using. This ensures that you have a complete copy of these support materials on your computer for future reference.

BIONUMERICS version 8.1 support materials:

• PDF tutorials for version 8.1
• PDF manuals for version 8.1

BIONUMERICS version 7.6 support materials:

• PDF tutorials for version 7.6
• PDF manuals for version 7.6

While the customer support for BIONUMERICS ends, the license for the software remains perpetual. At least in principle, this leaves the option to continue using the BIONUMERICS software without support. To prepare for this scenario, there are a number of things you can do before December 31^th, 2024:

• Make sure you are using the latest available build of your software version. For major version 8, this is BIONUMERICS 8.1.1, build 8.1.32234.42204. For major version 7, this is BioNumerics 7.6.3, build 7.6.13738.35510.
• Specific for version 7.6.3 users, make sure to download and install the NCBI SRA, EMBL ENA and CE Store uploader hotfixes.
• Download the setup file of the BIONUMERICS version you are using from our software archive. This will allow you to install BIONUMERICS again on another computer or to repair an existing installation in case installation files get corrupted.
• Note and write down your BIONUMERICS software license string. You will need the license string if you install BIONUMERICS on a new computer. The most recent license string was likely sent to you by email.
• Keep track of your USB protection key (dongle) or HASP soft-lock. Both options are equally safe and reliable. If you prefer, you can trade your HASP soft-lock key for a USB protection key, or vice versa, for network licenses.
• Download a copy of all PDF support materials for the BIONUMERICS version you are using. See our KB article on the bulk download of support materials for more information.
• If you are using wgMLST in BIONUMERICS version 8.1, make sure to install the WGS tools local plugin. Instructions on how to install this online plugin can be found in the hash-based whole genome MLST tutorial and in the plugin manual. The WGS tools local plugin enables you to run wgMLST analyses after the Calculation Engine is taken off-line.
• If you are using any of the species-specific genotyping plugins or the generic resistance detection plugin in BIONUMERICS version 8.1, download the online knowledge bases used by these plugins. For instructions on how to install the knowledge bases in a BIONUMERICS database, see our KB article on the use of genotyping plugins after the end of support for more information.

The species-specific genotyping plugins (for Escherichia coli, Listeria monocytogenes, Salmonella enterica and Staphylococcus aureus) and the generic resistance detection plugin download their knowledge bases from the BIONUMERICS support website. After December 31^st 2024, when the support website is taken offline, existing genotyping plugin installations will continue working with the same knowledge bases, but error messages might pop up if the plugin checks for updates online. For new genotyping plugin installations, an archive with all online knowledge bases should be downloaded and the corresponding knowledge bases installed manually. Please note that the ZIP archive only contains knowledge bases compatible with BIONUMERICS version 8.1, so make sure to have the latest software version installed.

Existing genotyping plugin installations:

• Open the genotyping plugin settings dialog and uncheck for each knowledge base the option "Check for updates on startup" and press <OK>.

You can keep working with the genotyping plugin with the same knowledge bases.

New installations of a genotyping plugin:

• Download the ZIP archive containing all online genotyping knowledge bases. Unzip the archive to a location on your hard drive. The "knowledgebases" base directory contains five subdirectories: GenotypingEcoli2, GenotypingListeria, GenotypingResistance, GenotypingSalmo, and GenotypingStaph for the Escherichia coli, Listeria monocytogenes, resistance detection, Salmonella enterica and Staphylococcus aureus genotyping plugin, respectively.
• Proceed with the plugin installation as usual. Several urlopen errors will appear "The server name or address could not be resolved" because the plugin tries to download its knowledge bases from the now offline website.
• Answer "No" to the question "Do you want to change the 'Listeria' genotyping settings now?"
• Close the BIONUMERICS database.
• Locate the source files directory for your database (the default location is the sourcefiles subfolder of the database directory). In the source files directory, there will be a directory called "GenotypingKnowledgebases" with a subdirectory that corresponds to the plugin you are installing (e.g., for the Listeria monocytogenes genotyping plugin, a directory "GenotypingListeria" will have been created by the plugin). Copy the content from the corresponding directory in the unzipped archive to the plugin folder in the source files directory.
• Open the BIONUMERICS database again.
• Open the genotyping settings. For each analysis that you want to perform, take following steps:
  • Press the <Change…> button to change the knowledge base.
  • In the dialog that pops up, highlight the preferred knowledge base and press <OK>.
• Press <OK> in the genotyping settings dialog.

The genotyping plugin is now ready for use.

Internet licenses will no longer be usable beyond December 31st, 2024.  

You will be able to trade in the internet license for a physical license dongle before the end of 2022, enabling you perpetual access to the latest version beyond December 2024.  

If the internet license is linked to a lease or evaluation license, you will not be able to access the software after December 31st, 2024. 

No, we will no longer maintain or support BIONUMERICS after December 31st, 2024. 

You can export your data in different formats, allowing them to be imported into alternative software programs. If you need access beyond 2024, perpetual licenses linked to an internet license will be allowed to be traded in for a physical license dongle before the end of 2022.  

We will no longer support or maintain BIONUMERICS or its resources beyond the end of 2024. Any support resources on the website will thus become unavailable after December 31st, 2024. 

The format recognized by BioNumerics/GelCompar II is an uncompressed gray scale TIFF file. An image editor is present in the software, supporting most known file types such as JPEG, GIF, PNG and compressed TIFF files in gray scale or RGB color. In this editor the files can be converted to an uncompressed gray scale TIFF file and added to the database:

1. Export the picture with your image software. 
2. Import your gel image in your BioNumerics/GelCompar II database: select "File > Import > Import gel file" and press the "Import" button.
3. Browse for your gel image and make sure the option "Open in image editor before import" is checked, press "Import".
4. In the Image editor select "Image > Convert to gray scale > Averaged" and select "File > Add image to database".

This message is produced when your gels are normalized using different reference systems, i.e. reference systems that have at least one different reference position, so that the reference systems can not be remapped automatically. In that case, you need to specify the molecular weight regression curves for both reference systems. Once the MW regression is known for both systems, the program will be able to remap the gels from one system into the other, and you will be able to compare the patterns in a Comparison window.

For defining regression curves, double-click on the fingerprint type, and then double-click on the reference system. If you entered the molecular weights for the names for the reference bands, you can simply choose Metrics > Copy markers from reference system, if not, you will have to enter the MW markers one by one.

Although your databases are listed in the startup screen, the software is unable to load the database since the path – saved in the .DBS file – does not correspond to the location of the database. To fix this error, the .DBS files in the Home Directory need to be modified:

1. Browse to the Home Directory and open the .DBS file of the database with a text editor such as NotePad.
2. On the second text line, the database path is specified. Update the path to the correct location*.
3. The .DBS file can now be saved and closed.

The above actions should be repeated for all .DBS files present in the database. Alternatively (and more convenient in case of many databases), a script is available to automate these tasks. Please contact us to obtain this script.

* From BioNumerics/GelCompar II version 5 on, the absolute database path in the database descriptor (.DBS) file is replaced by a relative “[HOMEDIR]” tag. Using this tag will make copying databases to another location easier.