Frequently Asked Questions

General

  • 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.).

    At Applied Maths 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, it is a service of Applied Maths to design specific scripts for you. 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.

  • Can I start with GelCompar II and upgrade to BioNumerics later?

    It is possible to migrate from GelCompar II to BioNumerics at any time, by paying the price difference. The databases of both software packages are compatible and interchangeable, with the understanding that GelCompar II will not be able to process any other data type than fingerprints.

  • How to cite one of Applied Maths' products?

    To correctly cite:

Installation

  • What are the system requirements for GelCompar II and BioNumerics version 6?

    The minimum hardware requirements for running the GelCompar II/BioNumerics version 6 application are the cumulative requirements needed to run the Operating System, the GelCompar II/BioNumerics application and optional database client software and third-party software that will run concurrently (e.g. Microsoft Office). The typical minimum hardware requirements for a computer running Windows XP, Microsoft Office XP and the GelCompar II/BioNumerics application are:

    • Processor: 1.30 gigahertz (GHz) processor or higher
    • Processor Type: Intel Pentium 4 or higher compatible processor
    • Memory: 512 MB or higher
    • Hard disk: 1 GB of free disk space (application files only)
    • Display: XGA (1024 x 768) or higher resolution monitor, True Color (32 bit)
    • USB port: Depending on the license type a free USB port may be required

    For standalone licenses, each computer that will run GelCompar II/BioNumerics must have an available USB port for connecting the Sentinel hardware security key. For network licenses, the computer that will be running the NetKey+ server program must have a free USB port for attaching the hardware security key. A 64-bit processor and Windows version are required for systems with more than 4 GB of RAM installed. The actual hardware requirements will largely depend on the features that will be used in GelCompar II/BioNumerics, the database platform used to store the GelCompar II/BioNumerics data and the size of the data. For example, the Power Assembler feature of the Sequence Types module requires a 64-bit processor and a minimum of 8 GB installed memory.

    The recommended hardware configuration for a computer running Windows Vista or Windows 7, and the GelCompar II/BioNumerrics version 6 application are:

    • Processor: 1.6 gigahertz (GHz) processor or higher
    • Processor Type: Intel Pentium Dual Core or higher
    • Memory: 2 GB or higher
    • Hard disk: 1 GB of free disk space (application files only), fast hard drive for storing database files (e.g. 7200 RPM SATA drive)
    • Display: SXGA (1280 x 1024) or higher resolution monitor, True Color (32 bit), graphics card with dedicated video memory

    When purchasing a new computer that will run GelCompar II/BioNumerics, make sure that you choose a 64-bit Windows version to allow for future memory expansion. At least 4 GB of RAM should be installed when purchasing a new system. A recent graphics card with dedicated video memory is recommended. Choosing a basic Windows theme instead of a Windows 7 or Vista Aero theme may be required if the computer is not equipped with sufficient dedicated video memory. Some features of BioNumerics may require hardware specifications that exceed the above recommedations. For example, the Power Assembler feature of the Sequence Types module requires a 64-bit processor and a minimum of 8 GB installed memory.

  • What are the system requirements for BioNumerics version 7?

    The minimum hardware requirements for running the BioNumerics 7 application are the cumulative requirements needed to run the Operating System, the BioNumerics application, the optional Database Engine and any third-party software that will run concurrently (e.g. Microsoft Office). The typical minimum hardware requirements for a computer running Windows Vista, Microsoft Office 2003 and the BioNumerics application are:

    • Processor: 1.6 gigahertz (GHz) processor or higher
    • Processor Type: Intel Pentium Dual Core or higher compatible processor
    • Memory: 2 GB or higher (1 GB if the Database Engine feature will not be installed)
    • Hard disk: 2 GB of free disk space (application files only)
    • Display: WXGA (1280 x 800) or higher resolution monitor, True Color (32 bit)
    • USB port: Depending on the license type a free USB port may be required

    For standalone licenses, each computer that will run BioNumerics must have an available USB port for connecting the Sentinel hardware security key. For network licenses, the computer that will be running the NetKey+ server program must have a free USB port for attaching the hardware security key. Alternatively, a software protection key (Softlock) could be used. A 64-bit processor and Windows version are required for systems with more than 4 GB of RAM installed. The actual hardware requirements will largely depend on the features that will be used in BioNumerics, the database platform used to store the BioNumerics data and the size of the data. For example, the Power Assembler feature of the Sequence Types module requires a 64-bit processor and a minimum of 8 GB installed memory.

    The recommended hardware configuration for a computer running the latest Windows and Office versions, and the BioNumerics 7 application are:

    • Processor: 1.8 gigahertz (GHz) processor or higher
    • Processor Type: Intel Core 2 Duo Processor or higher compatible processor
    • Memory: 4 GB or higher
    • Hard disk: 2 GB of free disk space (application files only), fast hard drive for storing database files (e.g. 7200 RPM SATA drive)
    • Display: WXGA+ (1440 x 900) or higher resolution monitor, True Color (32 bit), graphics card with dedicated video memory

    When purchasing a new computer that will run BioNumerics, make sure that you choose a 64-bit Windows version to allow for future memory expansion. At least 4 GB of RAM should be installed when purchasing a new system. A recent graphics card with dedicated video memory is recommended. Choosing a basic Windows theme instead of a Windows 7 or Vista Aero theme may be required if the computer is not equipped with sufficient dedicated video memory. Some features of BioNumerics may require hardware specifications that exceed the above recommendations. For example, the Power Assembler feature of the Sequence Types module requires a 64-bit processor and a minimum of 8 GB installed memory and a fast storage system (SSD).

  • 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.

  • 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.

Database

  • 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 file 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.

Sequences

  • 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.

Troubleshooting

  • 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.

  • 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.

    Solutions:

    • 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. 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.