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
A tripal module for Chado phylogeny tables, developed for http://legumeinfo.org/.
Extension Module
A module for management of QTL data. This module provides pages for QTLs, loaders, and relies on a controlled vocabulary developed by representatives from the Dorrie Main lab (CoolSeasonFoodLegumes, Genome Database for Rosaceae, CottonGen), the LIS group (PeanutBase, and LegumeInfo), and others. Two "placeholder" modules are in use by the two organizations. A unified module will be developed when Tripal 3.0 is released. A data dictionary for defining and describing QTL has been developed, along with a Chado data mapping.
Extension Module
Tripal Alchemist is an entity management interface for Tripal 3. You can convert your Chado entities from one bundle type to another. Includes collections integration for fast and easy conversion of large, complex entity sets.
Extension Module
Tripal Analysis Expression modules allows users to upload a differential expression analysis, including expression values for a feature across many biomaterials (such as RNASeq libraries or microarrays). Loaders include a biosample xml loader and an expression data loader. The expression levels are visualized on the individual feature field as a bar chart, or, users can collect multiple features and view them in a heatmap. A field is included that will allow CSV download of expression data when attached to the organism, analysis, or individual feature.
Extension Module
This module is responsible for displaying reports from Gene Ontology (GO) analyses. This module contains a Gene Ontology Annotation Format (GAF) file loader to import GO terms assigned to features. Otherwise, GO assignments must already be loaded into the Tripal database using other data loaders (e.g. using the Tripal InterPro Analysis module or a GFF file)
Extension Module
This module extends the Tripal Analysis Module and provides visualization of Unigenes derived from ESTs. Currently, a web-based loader is not available, however, once a unigene is loaded into Chado, this module will provide listings of available Unigenes constructed for each organism and link features to their respective Unigenes.
Extension Module
This module extends the Tripal Analysis Module that comes with Tripal, and provides loaders and viewers for BLAST results. It does not provide a service for performing BLAST analyses. This module imports BLAST results in XML format, and supports any number of database FASTA file formats. It natively supports NCBI and ExPASy formats, but allows for support of custom formats as well. Features that are loaded into Chado will automatically have BLAST results associated and results will be visible on the feature's page.
Extension Module
This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+. It supports blastn, blastx, blastp and tblastx with separate forms depending upon the database/query type. It provides a simple interface allowing users to paste or upload a query sequence and then select from available databases. Additionally, a FASTA file can be uploaded for use as a database to BLAST against (this functionality can be disabled). Results are provided in a tabular listing with alignment information and are available for download in multiple formats (HTML, TSV, XML). This module integrates with the Tripal Jobs system providing administrators with a way to track BLAST jobs and ensure long running BLASTs will not cause page time-outs. BLAST databases are made available to the module by creating Drupal pages describing them. This allows administrators to use the Drupal Field API to add any information they want to these pages. BLAST database records can be linked to an external source with more information (ie: NCBI) per BLAST database.
Extension Module
This module provides the ability to start a Daemon that executes Tripal Jobs. By default, jobs in Tripal's job queue are executed either manually using Drush or via the UNIX cron. However, at most cron can only execute once every minute. The Daemon allows jobs to execute once they are submitted. This is particularly useful if you are allowing non-Tripal Administrators to submit jobs such as is the case with the BLAST UI module.
Extension Module
This module supports sequence similarity search on a Tripal website through a new dual application option. The Tripal module provides access to the speed increase available through Diamond for BLASTP/BLASTX style searches as well as traditional NCBI BLAST for BLASTN. Both applications are integrated into a single interface that provides file upload or copy/paste sequence support for the query and access to formatted databases for NCBI BLAST or Diamond. The target databases can be customized for the categories of whole genome, gene, protein, and transcriptome/unigene. The administration interface allows the admin user to set what pre-indexed databases are available (which show up in a dropdown menu). The module supports execution of the searches on a remote machine so that the search is not running directly on the limited resources typically associated with web servers.