GANT Plugins and Drivers

Welcome! Here you can find drivers and plugins to use with our extensible gene browser, GANT.

Installation Instructions

Click the download icon of your desired plugin or driver and then choose Save to Disk. Do not choose Open with Java. Save to Disk Image

Save the file to the appropriate location:

For plugins, save the file to the "plugins" folder of your application directory
For drivers, save the file to the "lib" folder of your application directory.

Then, simply restart GANT and follow the directions under "Options > Intro Wizard " to setup your new plugin!

GANT Plugins

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

Genomic Plugins

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.

Name	Download Link	Acadmic Price	Corporate Price
Ensembl	Download ensembl-genomic.jar >>	FREE!	FREE!
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
TrAPSS	Download trapss-genomic.jar >>	FREE!	FREE!
For users of the TrAPSS LIMS system, this plugin will load sequence data from the TrAPSS database. You will be able to search for and load any gene that is in the projects and sets to which you have access. For more information about TrAPSS, please visit http://public.eng.uiowa.edu. Required Driver: TrAPSS Modules Required Driver: MySQL J Connector
UCSC	Download ucsc-genomic.jar >>	FREE!	FREE!
The UCSC data source will load sequence data from the UCSC database available here: http://genome.ucsc.edu. Required Driver: MySQL J Connector

Annotation Plugins

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.

Name	Download Link	Acadmic Price	Corporate Price
ConSeq Web Resource	Download conseq-web.jar >>	FREE!	FREE!
This plugin connects to the ConSeq web resource to retrieve predictions of functionally and structurally important residues.
Ensembl Protein Features	Download ensembl-protein-features.jar >>	FREE!	FREE!
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
Ensembl Variation	Download ensembl-variations.jar >>	FREE!	FREE!
This plugin will retrieve all gene variations (polymorphisms) from Ensembl. Required Driver: MySQL J Connector Required Driver: Ensembl J Connector
Methylator	Download methylator.jar >>	FREE!	FREE!
This plugin connects to the Methylator web resource at Harvard to retrieve DNA Methylation predictions. The predictions are SVM-based. The threshold has been set to -0.455 (default). For more information, visit http://bio.dfci.harvard.edu/Methylator/about.html.
nnPredict	Download nnpredict.jar >>	FREE!	FREE!
This plugin connects to the nnPredict web resource to retrieve peptide secondary structure predictions.
Phobius	Download phobius.jar >>	FREE!	See Description
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.
Sequence Analysis	Download sequence.jar >>	FREE!	FREE!
This plugin performs simple sequence analysis on the gene sequence such as detecting C-G dinucleotides.
TrAPSS Annotation	Download trapss-annotation.jar >>	FREE!	FREE!
For users of the TrAPSS LIMS system, this plugin will load annotation (including primers) from the TrAPSS database. For more information about TrAPSS, please visit http://public.eng.uiowa.edu. Required Driver: TrAPSS Modules Required Driver: MySQL J Connector

GANT Drivers

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

Name	Download Link
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 and is used in conjunction with the MySQL J Connector. The Ensembl J Connector is published under the LGPL.
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/. The connector is distributed under the GPL license.
TrAPSS Modules	Download trapss-modules.jar >>
This connector provides all the necessary information for connecting to and obtaining information from the TrAPSS LIMS database. It is needed when you use any of the TrAPSS plugins and is used in conjunction with the MySQL J Connector.

Your Application Directory

The default* GANT application directory is located:

Windows XP and older "C:\Program Files\BioNeos\GANT\"

Windows Vista "C:\Users\<user>\AppData\Local\VirtualStore\Program Files\BioNeos\GANT\"

Max OS X "/Users/<user>/Library/BioNeos/GANT User Data/"

Linux "/home/<user>/BioNeos/GANT/"

* 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.