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Welcome!   Here you can find drivers and plugins to use with our extensible software solutions.

Be sure to save the drivers to the "lib" folder of your installation directory and the plugins to the "plugins" folder of your installation directory.

For more information on drivers and plugins, please view the help documentation.
    Bio::POD Drivers
 

Note NOTE: Download these to the "lib" folder of your installation directory.

MySQL J Connector Download mysql-connector-java-3.1.11-bin.jar >>
This connector provides the necessary tools for connecting to a MySQL database. If you want to get a different version than the one provided here, you may obtain the connector at http://dev.mysql.com/downloads/.
Ensembl J Connector Download ensj-36.1.jar >>
This connector provides all the necessary information for connecting to and obtaining information from Ensembl's database. It is needed when you use any of the Ensembl plugins below and it used in conjunction with the MySQL J Connector. If you want to download a different version of the Ensembl Connector, visit http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensj-web/build/. The Ensembl J Connector is published under the LGPL.

    Bio::POD Plugins
 

Note NOTE: Download these to the "plugins" folder of your installation directory.

Genomic Plugins

Question What are Genomic Plugins?
Genomic plugins grant access to data sources to retrieve and display all the necessary genomic information including the nucleotide sequence, exons and introns, the location of the start and stop codon, and the peptide sequence.
Ensembl Download ensembl-genomic.jar >>
The Ensembl data source will load sequence data from the publically accessible Ensembl Project located at http://ensembl.org/ . You will be able to load any of the same data that you could access through the Ensembl webpage.
Required Driver: MySQL J Connector
Required Driver: Ensembl J Connector

Annotation Plugins

Question What are Annotation Plugins?
Annotation plugins grant access to data sources to retrieve and display different types of annotation. For example, some may retrieve SNPs and others may retrieve conserved domains.
Phobius Download phobius.jar >>
This plugin connects to the Phobius web resource to retrieve transmembrane topology and signal peptide predictions. Phobius is freely available for academic use. For commercial use, please contact Brunak Research at the following e-mail address: jan@brunak.dk.
nnPredict Download nnpredict.jar >>
This plugin connects to the nnPredict web resource to retrieve peptide secondary structure predictions.
Ensembl Variation Download ensembl-variations.jar >>
This plugin will retrieve all gene variations (polymorphisms) from Ensembl.
Required Driver: MySQL J Connector
Required Driver: Ensembl J Connector
Ensembl Protein Features Download ensembl-protein-features.jar >>
This plugin will retrieve all protein features from Ensembl. Examples: functional domains, transmembrane domains, and coiled-coil domains.
Required Driver: MySQL J Connector
Required Driver: Ensembl J Connector


    Your Installation Directory
 

The Bio::POD installation directory is located:
Windows"C:\Program Files\BioNeos\BioPOD\"
Max OS X"/Applications/BioNeos/BioPOD/"
Linux"/home/<user>/BioNeos/BioPOD/"

Note: During the installation process you are allowed to modify the installation directory of the application from its default location. If you did so, then your copy of the application may be located in a different location from what is mentioned above.


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