Tripal Extensions

The following is a list of extensions that have been provided by Tripal site developers and which can be imported into another Tripal site. If you have custom extensions you would like to share, please let us know by joining the Tripal mailing list and sending a request. Consider adding your extensions even if only in development state as this encourages collaboration and reduces duplication of effort. Use the fields below to filter.
Extension Module
This module extends Tripal to support association of files with data stored in the Chado database. The module will also provide an API to allow other modules to create "plugins" for specific file types. The module is still in development but it is expected that it will provide plugins for Images, BAM and VCF files. These plugins will provide the functionality for visualization and access to these types of files. This file is of importance to the future Tripal Exchange module will provide web services for data house in Chado and in files.<p>
Extension Module
This module extends the Tripal Analysis Module that comes with Tripal, and provides loaders and viewers for InterProScan v4 and v5 results. It does not provide a service for performing InterProScan analyses. This module imports results in XML format. Features that are loaded into Chado will automatically have InterProScan results associated and results will be visible on the feature's page.
Extension Module
This module exposes Chado as a JBrowse-compatible REST API.
Extension Module
This module extends the Tripal Analysis Module that comes with Tripal, and provides loaders and viewers for results generated using the KEGG/KAAS tool at http://www.genome.jp/tools/kaas/. It does not provide a service for performing KEGG analyses. This module imports results in the KEGG hier format. Features that are loaded into Chado will automatically have KEGG Orthologs and Pathways associated and results will be visible on the feature's page. A KEGG report is also made available on the KEGG analysis page allowing the user to browse all the results from the entire analysis. Note: KEGG has recently stopped offering the heir file format from it's service. Therefore this module is currently only useful for older files.
Extension Module
Supports multiple Chado instances in one Tripal installation. Chado instances must be in the same database in different schemata. By default, Chado instance selection is made on a user basis: the administrator can enter in the system the connection information for several Chado databases and assign to each user a specific Chado connection setting. However, a companion module, included with this module, allows users to select which instance of Chado they want to use through a Drupal block dropdown menu. Note: it's also possible to only use one Chado instance with different user accounts to access to that database. Why multiple Chado instances? There are many reasons and just to give a few: private/public sites, dev/staging/prod, multiple organisms, multiple versions of genomes,... With the multi-chado module, all thoses instances can share a same common Drupal site (configured and with the same users of course).
Extension Module
Supports management of network data, in particular for gene co-expression data. This module is in use on the GenNetEngine. It is still currently being revamped for general use.
Extension Module
This module provides d3.js integration for Tripal with the intent of providing common biological diagrams such as: Pie &amp; Bar charts (Coming Soon), Sequence Coordinate Diagrams (ex: BLAST Hit diagram; Coming Soon), Pedigree Diagrams
Extension Module
This module enables functional testing on Tripal extension modules through Drupal Simpletest module (Drupal core). Examples of .test file can be found here: * https://github.com/tripal/tripal_dt/blob/master/tripal_dt.test * http://cgit.drupalcode.org/tripal_cvb/tree/tripal_cvb.test?h=7.x-1.x * http://cgit.drupalcode.org/brapi/tree/brapi.test
Extension Module
TripalMap module displays map data stored in Chado. The module provides interfaces to view all linkage groups of a map, choose a linkage group and zoom in to a specific region of a linkage group, compare maps that share the same markers, change colors of markers/QTL, etc. The interface can be integrated in Tripal map page and hyperlinked to/from any Tripal page that are displayed in maps (marker, QTL, heritable morphological marker and/or gene). The admin page will allow site developers some flexibility of the display pattern. The map display is built from the data in Materialized Views for both better performance and flexibility of the way the data is stored in Chado. The admin page will allow using a custom query for building materialized views. The module will allow Tripal based databases to provide users functionality similar to GMOD-CMap without having to maintain a separate underlying database.

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