Frequently Asked Questions

BIONUMERICS phasing out

  • If I e-mail or call for BIONUMERICS support, will you reply?

    Until the end of December 2024, absolutely.  After December 31st, 2024, we will no longer offer BIONUMERICS support, though we will continue to develop, offer and support other solutions going forward. 

  • I have bought a BN8 license and this included a free workshop registration. Will there still be workshops organized? 

    We will launch a support platform that will be available for the next three years. This will allow clients with a BIONUMERICS license under support contract to access all training and workshop materials, and have these available at any time. For the year 2022, two (online) workshops will be scheduled, but no in person workshops.  

  • What will happen with the public BIONUMERICS Calculation Engine? Will I still be able to use it for analyses after 2024?  

    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.

  • Are there any alternatives to BIONUMERICS you can recommend to us? 

    At this moment, unfortunately not.

  • At what moment will I no longer be able to buy credits for the BIONUMERICS Calculation Engine? 

    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. 

  • For wgMLST specifically, how will I be able to compare any results obtained before 2024 with results obtained afterwards?    

    We will make available a solution in BIONUMERICS that allows you to use your databases and wgMLST results beyond 2024, enabling comparison of wgMLST results previously run on the Calculation Engine versus locally obtained results. We anticipate a functionality where one no longer relies on shared allele nomenclature, but rather using an efficient hashing implementation used for sequence comparison. This way, a BIONUMERICS user will have access to a functionality converting their wgMLST databases from a sequence-based to a hash-based analysis tool, no longer relying on central allele nomenclature, but nevertheless providing interchangeable results between different databases and users.  

  • Is there a convenient way to download all PDF tutorials and manuals?

    The BIONUMERICS support website will be taken offline on December 31st, 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:

    BIONUMERICS version 7.6 support materials:

  • Will the genotyping knowledge bases be maintained after 2024?  

    No, we will do no further maintenance or support on BIONUMERICS or its components after December 31st, 2024. 

    While no knowledge base updates will be provided after 2024, you will still be able to continue using the genotyping functionality in existing BIONUMERICS databases, provided that the genotyping plugin was installed in the database before the end of 2024.   

  • How can I best prepare myself for the BIONUMERICS end of support?

    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 31th, 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.
  • Will the genotyping changelogs remain accessible on the BIONUMERICS website after 2024? 

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

  • Can I still use the species-specific genotyping plugins after the BIONUMERICS support website is taken offline?

    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 31st 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.

  • What happens to the hundreds of credits I have purchased that are currently unused?

    Credits can be purchased until the end of 2023, enabling you to spend any purchased credits during one full year. Any unused credits will be lost after December 31st, 2024.

  • I am using an internet license, will I still be able to use this type of license after 2024? 

    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. 

  • I am using a HASP license, what if I want to move this type of license or upgrade the hardware the license is running on after 2024? 

    The HASP license is linked to the physical server characteristics. We cannot update these licenses and as such, support any hardware changes after December 31st, 2024. Transfer of HASP licenses can be executed as documented in the BIONUMERICS installation manual. 

  • What happens if my USB is broken/stolen/lost after 2024? Can I still get a replacement key?  

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

  • Will the installation files of the different BIONUMERICS versions still be available for download after 2024? Eg. after switching computers, the installation files are needed.     

    No installation files will be available after December 31st, 2024 as we will no longer maintain or support BIONUMERICS websites past that date.

  • I’m running an annual subscription (BN internet license), how will I have access to my data after 2024? Where/how can I extract my data? 

    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.  

  • When buying CE credits in bulk, you stated there was no expiry date for usage of these credits. Will you reimburse the unused credits after 2024?   

    Credits can still be used until December 31st, 2024 and new credits can be purchased until the end of December 2023. Any unspent credits after December 31st, 2024 will not be reimbursed. 

  • Will the tutorials, tutorial movies, FAQ and other support resources still be accessible after 2024?

    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. 

  • Will the online help, accessible from within the BIONUMERICS software, still be available after 2024? 

    No, we will no longer offer BIONUMERICS maintenance or support after December 31st, 2024, including the online help. However, before the end of 2024, the PDF files can be downloaded from within the software for future reference.


  • How to cite your software products?

    To correctly cite:

  • Would it be possible to adapt the software to meet our specific needs?

    Flexibility is offered by the script language of our software packages and the Python® programming language. These programming languages contain a large array of specialized functions that allows one to customize the software to a considerable degree (e.g. automation of specific tasks, import of own data formats, etc.).

    We already have a library of scripts for frequently requested and useful additional functions, and it is likely that your requests are already available in one or more scripts. If not, we can design specific scripts for you as a service. Depending on the specificity or the complexity of the request, we may offer you the script(s) for free or at a certain agreed charge. Features that are not achievable using scripts will be implemented in the code of the software, if considered of general interest.

  • How can I gain access to all the resources on the website?

    In order to get access to the content of the technical support website you need to fulfill two requirements. First, you need to have an active support contract or evaluation license. Second, you need to register an account on the website. This can be done by navigating to the register page and fill in some details, such as name, e-mail and your software serial number. After registration you will receive a confirmation e-mail and password. Using these credentials you can then log into the support website through the login page.   


  • Which operating systems are supported?

    Our software licenses are supported on most Windows operating systems depending on the time of release of the software version and the OS. Some of our customers are running the software on other operating systems, but we do not officially support this.

  • How to install a standalone license?

    Detailed installation instructions can be found in the installation guides, which can be downloaded from Download manuals & tutorials page.

  • How to install a network license?

    Detailed installation instructions can be found in the installation guides that can be downloaded from the Download manuals & tutorials page.

    In summary: The NetKey+ server program and Sentinel drivers must be installed on the computer where the hardware security key will be connected to (i.e. the server computer). After installation of these features on the server computer, the service needs to be installed and started using the NetKey+ Configuration tool. Once started, the licenses can be configured. On the client computers, a standalone license of the software should be installed.


  • Can multiple users access the same database, and at the same time?

    If you want multiple users to access the same database, make sure the database is located on a shared network drive, and change the Home Directory of each user to this location.

    If you want multiple users to access the same database at the same time, this request has further requirements:

    • The users need to be able to work with the software at the same time. This is possible through a multi user network license or multiple standalone licenses.
    • The database should be a connected database, with the database located on a shared network drive.
    • The Home Directory must be set to the local machine of each user, with the path directed to the connected database which is on the network location. 
  • Which database engines are supported?

    When a new database is created in version 5 or 6 using the default settings, a connected Microsoft® Access database is created. When a new database is created in version 7 using the default settings, a Microsoft SQL Express® database is created (under conditions that the BioNumerics database engine was installed and the home directory is located on a local drive).

    Other supported database engines are SQLite (from BioNumerics version 7.5 on), Microsoft® SQL Server (version 2005, 2008 and 2012), Oracle® (version 9i, 10g and 11g), and MySQL (version 5.x). Other database engines may work but are not guaranteed to be fully compatible in a standard setup.

  • What type of gel files is supported?

    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".
  • How to import and process a gel file?

    In the online help, a complete chapter is dedicated to this topic. A training video and tutorial is also available.


  • How can I import sequences in batch in my database?

    Sequences present as flat text files, as well as binary chromatogram files from Applied Biosystems, Beckman, and Amersham automated sequencers can be imported and assembled in batch in BioNumerics. A training video and tutorial are available.


  • When I try to open a database, following error message appears: "Unable to open the database. Error code 5: Access denied."

    The error code 5 message pops up when the software is unable to open the database because the files in the database folder are specified as being “read-only”. To solve this, navigate to the path where the database is located, right-click on the database folder and uncheck the option “Read-only”. Confirm that you want to uncheck this option for all files and folders in this database folder.

  • When I open a TIFF file the program tells me “Invalid TIFF file. Invalid tag 'samplesperpixel'.” What does that mean?

    This message is produced because the type of file is not valid. The format recognized by the software 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.

    In case the error still appears in the image editor, the TIFF file might have transparency enabled. Similar to many other programs, BioNumerics does not support transparent TIFF files. The solution is then to open the file in e.g. Photoshop and disable the transparency feature.

  • The message "Unable to remap reference system" is displayed in the Comparison window. Why do I see this message instead of the gel lanes?

    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.

  • When I try to open a database I receive the error message "Invalid or absent protection key."

    This error is displayed if:

    • The protection key is not attached to the (server) computer
    • The protection key is attached to the (server) computer, but the dongle drivers are not (properly) installed.
    • The license string entered in the startup screen is not compatible with the attached key.


    • Check if the protection key is attached to the (server) computer.
    • Run the check SN tool on the computer with the key attached. If the serial number of the key is displayed, the key is recognized. If the key is not recognized, you can download and install the latest Sentinel drivers from the Sentinel website. Choose the Windows operating system option 'Sentinel System Driver Installer for Sentinel SuperPro, UltraPro & SHK'. Make sure you have sufficient privileges to install the drivers on the computer. During installation the key should not be attached to the computer, after installation the key should be attached again.
    • Check the license string entered in the startup screen.
  • When I try to open a database, following error message appears: "Unable to open the database. Error code 3: The system cannot find the path specified."

    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.

  • How do I change my Home Directory?

    The location of the Home Directory may be established during the installation of the software. At any point after this, it may be changed via the Startup screen.

    • In versions up to and including version 4.6, the Home Directory may be changed by selecting the “Home directory” (or “Homedir”) button in the Startup screen, and in the browser window, browsing for and selecting the folder which contains your database(s).
    • In version 5.0 and beyond, this is done in the Startup screen by selecting Settings > Change home directory. From here you can choose one of the two default suggested locations for your Home Directory, or choose a custom folder of your choosing.

    All databases that are present in the Home Directory will be listed in the startup screen. New databases will automatically be stored in the Home Directory and will be listed in the startup screen.