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Installation Guide for Windows
There is no need to shut down other applications in order to install the software, however doing so increase the speed of your installation.

Insert the CD into the drive. The BioBind licence will automatically appear. If you are still running other applications, the Licence window may appear behind other active windows. Minimise these to access the BioBind application.

Licence
The BioBind Licence is a legal document that must be accepted in order to continue with the installation of your BioBind software. Declining the licence will result in termination of the installation.
Licence Key
You will find your BioBind License Key on the back of the booklet accompanying your software CD.

Your BioBind software will only function using a valid 32 character licence key. If the key fails to validate, check that all numbers are zero and not the letter O. Should you have entered an invalid key, an error message will appear. If you have checked the above and your key still fails to function, please contact us.

Proxy Settings
On most systems, web pages are retrieved directly from the internet. Most home users will not access the internet using proxies and should leave the fields blank. However, some sites have a central server and the site policy insists that web pages are accessed through the server. Such a server is known as a proxy and can cache frequently queried web pages to improve search efficiency. The server is accesseed by specifying a name and a port. A port is a doorway into the computer. The most common port for web access is 8080.

In most cases the proxy looks something like wwwcache.institute.ac.uk:8080 for institutes or wwwcache.company.co.uk:8080 for companies.

Proxy information is available from the web browser. A variety of commonly used web browsers is listed below together with instructions for retrieving proxy data. Access this information and type it into the BioBind Proxy Settings window.

    Internet Explorer

    Open the Tools menu and access Internet Options. Select the Connections tab and then the LAN settings button. If you require a proxy, the Advanced button under the Proxy Server section will be accessible. Click this button and type into the BioBind Proxy Request Field the Proxy address to use information followed by a colon (:) and then the Port number for both the HTTP field and the FTP field.

    Netscape

    Open the Edit menu and select Preferences. Click on the arrow next to Advanced and highlight Proxies. Copy the information in the HTTP Proxy field followed by the information in the Port field. Do the same for the FTP field.

    Mozilla

    Open the Edit menu and select Preferences. Click on the plus sign next to Advanced and highlight Proxies. Copy the information in the HTTP Proxy field followed by the information in the Port field. Do the same for the FTP field.

    Opera

    Open the Tools menu and select the Preferences option. Choose the Network option from this sub menu and then Proxy Servers. Copy the relevant information from the HTTP and FTP fields.
Additonal Downloads
BioBind does not distribute some EMBASSY packages or data which have potentially restrictive licencing conditions. If use of this data is allowed at your site then leave the selection boxes checked, otherwise de-select them. Please see our EMBASSY page for further details.
Cygwin Setup Wizard
Cygwin emulates the EMBOSS native environment on a Windows operating system. For those wishing to delve more deeply into computing and bioinformatics, it also provides a total Unix environment in which to work (using the bash shell by default). To proceed through the installation, select an option on each of the windows presented to you and click Next .

    Download Source

    As this is not a straightforward cygwin installation, but a customised one, the correct selection here is Install from Local Directory

    Root Install Directory

    This is the directory where the cygwin will be installed and it is recommended that a cygwin folder be created by typing Cygwin as the final folder name on the path where you have chosen to install your BioBind software. By default the CD will select your local home directory (the one you log on to). If this is not the correct directory, you may alter it using the Browse button.

    Default settings are to create this directory for All Users on one machine. If you want it to be available to just yourself, select the Just Me option.

    The default file type is Unix as cygwin is an Unix emulator. Selecting the DOS option means that any files will be written in the format of the Windows operating system.

    Local Package Directory

    This is the directory which contains all the information needed for your BioBind software installation. Assuming D is your CD drive, then the correct path should be D:\emboss\release. If this does not display automatically, use the Browse button to select the CD drive and explode the emboss directory by selecting the plus sign. Highlight the release directory and hit OK. When clicking Next > on this screen, there may be a short delay whilst the files are accessed.

    Select Packages

    The default selection here is curr or the current directory and is correct. This is to ensure that the contemporary version of Cygwin is installed. It is this version that is compatible with the BioBind software.

    Installation

    The software will now be installed on your machine. This will take approximately 25 minutes. Progress is monitored as the Total installation and what proportion of the disc space has been filled. Each Package is also displayed as the percentage installed. A percentage count in the cygwin toolbar represents the total installation.

    Create Icons

    Once the software has been installed, select any icons to be displayed. By default icons are selected for the Desktop and the Start menu. De-select any that are not required. Hit the Finish button.

    Installation Complete

    This message will tell you that your installation is complete. If you are installing a new version, and the final message states that "Nothing needed to be installed" you still have files left from an old installation which must be deleted.
Additional Downloaded Packages
Any additional downloads selected prior to install may now be prepared. In order for the software to be retrieved, you must be connected to the internet. Once connected, double click on a Cygwin icon to open the window. Type emboss-extra into the window and hit the enter key. This will download and install all additional packages requested.

If you have Windows 98 or Windows ME, it is imperative that you are connected when you install the initial software, otherwise each additonal package must be retrieved individually after the installation is complete.

Accessing EMBOSS
Type the name of an EMBOSS program at the prompt in either the Cygwin window, or the white RVXT window that appears when Jemboss is automatically started. The program will be recognised by either window.
Accessing Jemboss
Double click on the Jemboss icon on the desktop. This will automatically launch the interface.
File Location
All files that are saved in cygwin by default will end up in directory\cygwin\home\login. Where directory is the folder that you installed cygwin into when you were setting up the software and login is your local home directory - by default the one you are in when you log on to your computer.
Uninstalling your BioBind software
Should you upgrade to a new version of the software, you must first remove the old installation. To do this follow the instructions below:

  • Drag the cygwin folder from your computer to the recycle bin.
  • Drag any cygwin desktop icons and start menu items to the recycle bin.

  • Re-insert your BioBind Software CD (either the original one or a new one)
  • Select "My Computer" and right click on the CD drive
  • Select the Open option to access the CD contents
  • Double-click on the tidyreg icon

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