The Java SDK 1.4 is a pre-requisite for successful installation of your BioBind software. We recommend the Blackdown port for linux. Alternatively the SUN microsystems version may be used.

Your server should already have a web server installation. Apache Tomcat is included as part of the BioBind installation.

Your BioBind software supports the use of Generic NQS or OpenPBS batch queueing systems. Should you have a different system installed on your server, please contact us.

Login as Root to the machine that will be running the Jemboss server.

Set up a user account biobind on the server. Tomcat is installed by your BioBind installation wizard and run as the non-priveleged user "biobind".

Insert the CD into the drive. To launch the install wizard execute the install script by typing

cd /mnt/cdrom/install

at the prompt. The mountpoint may be different depending on the hardware and Linux distribution.

Your BioBind software will automatically search for the Java installation in the most obvious places. Should it fail to find it, you will be prompted for the exact path of the Java location on your machine.

In most cases the proxy will look 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.

Konqueror

Open the Settings menu and select the Configure Konqueror option. Choose the Proxy icon from the scroll list on the left hand side of the window. On the Proxy tab on the right hand side ensure that the Use Proxy option is checked. (If it isn't checked and you are otherwise connected to the Internet, then you do not need a proxy for your machine) Follow one of the Setup buttons. Copy the relevant information from the HTTP, FTP and Port fields.

Use unix authentication

This box is checked by default and specifies that users must provide a username and password at login to the server. Uncheck this box if you do not require this option.

IP address

The information required here is the IP address of the server to which your users will log in. By default it is set to the server's IP address and should not need changing unless it is incorrect.

Use Data Encryption

This option is selected by default and encrypts data transfer between the client and server. It is the recommended setting. Uncheck the box if you do not wish to use Secure Socket Layer (SSL) / HTTPS encryption.

Port

This information relates to the port used to access the services for Tomcat and the Jemboss results directory. The default port is 8443 for a secure connection (HTTPS) and 8080 for a non-secure connection (HTTP).

The default Tomcat installation directory is /usr/local/tomcat

The Jemboss Results Directory is where the EMBOSS applications are run and every result stored. By default it is located at /tmp/SOAP/emboss. It is highly recommended you change this as this directory is often removed on rebooting.

Provide Password

The password enables the client access to the server and should be at least six characters long.

Organisation Name

Name of the organistion to whom the BioBind software is licensed. This is the name that will appear on the authentication certificate.

Location

This information will also appear on the authentication certificate and should indicate the location of your organisation.

Country

Set by default to UK this can be altered by placing the cursor inside the text box. This information will also appear on your authentication certificate.

Days until Expiry

This sets the expiry information for the SSL certificates. Once these have expired, Tomcat is no longer accessible. It is recommended that these certificates are updated regularly for security purposes. The default setting of 365 days can be altered. There is no specified maximum limit.

No queueing sytem

This is the default setting and if no queuing system is selected, this option will run your software as a background process on the server.

OpenPBS or Generic-NQS

If authentication has been selected then either of these options will elect to submit batch processes to the network queueing software supported by the BioBind software. If you have a different batch queue system, please contact us.

• EMBOSS - Sequence analysis package. Approx. 13.6 MB
• PHYLIP - EMBASSY phylogeny package. Approx. 312.2 KB
• ESIM4 - cDNA/Genomic alignment application. Approx. 47 KB
• DOMAINATRIX - EMBASSY 3D structure package. Approx. 165 KB
• Primer3 - EMBASSY primer design application. Approx. 233 KB
• PRINTS - Protein motif database. Required for pscan. Approx. 22.8 MB
• Rebase - Restriction enzyme database. Required for all restriction applications. Approx. 304.2 KB
• aaindex - Amino acid biophysical properites index. Approx. 159.1 KB

To set up the BioBind web launch page for your new bioinformatics web services, there are 2 final steps:

To start and stop the Tomcat server, the commands tomstart and tomstop should be executed as root. This launches Tomcat as the user biobind. To halt the server, the command tomstop must be used as Root.

• Access the script from /usr/local/emboss/bin/tomstart
• Edit the JAVA_OPTS variable by adding the Java Vitual Machine option -Xmx to specify a suitable memory size: e.g.,

  setenv JAVA_OPTS “-Djava.library.path=/usr/local/emboss/lib -Xmx1500m”

  to set a memory size for the server of 1500Mb.

Login as Root and re-insert your BioBind Software CD (either the original one or a new one). If your mountpoint is /mnt/cdrom type

/mnt/cdrom/scripts/uninstall and the old software will be removed. If your mountpoint is different, replace /mnt/cdrom with the relevant path.

This uninstalls both the EMBOSS/EMBASSY/Jemboss applications and the Tomcat web launch software and takes approximately 1 minute.