Difference between revisions of "Tripal"

Revision as of 23:26, 5 September 2012

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About Tripal

Tripal is a web front end for Chado databases, based on the Drupal content management system. Tripal leverages many of the features of Drupal--ability to search and edit content, detail pages for different types of content, customizable page layouts, and so on--to provide users with an intuitive, flexible interface to a database.

Features and advantages of Tripal:

• Allows rapid development of an online genomic database.
• Site administrators can add non-biological content to their sites and allow editing of content by non-technical users.
• Integrates directly with GMOD Chado.
• Provides visualizations for Chado "modules" such as features, analyses, libraries, stocks, and others.
• Provides an interface for easy editing/updating of data in Chado.
• Provides full text and categorical search capabilities for Chado content.
• Can integrate GMOD tools such as CMap and GBrowse.
• Integrates with powerful Drupal features like Drupal views and panels
• Provides fully customizable PHP-based templates to allow users to change the look and feel of their installation
• Web-based management of Chado (i.e. installation of Chado v1.11 and loading of ontologies)
• Loaders for GFF3 and FASTA format files.
• Provides an API to allow for creation of custom extensions by anyone.

Visit the Tripal website.

Downloads

Download Tripal: http://tripal.sourceforge.net/?q=download

The latest development version of Tripal is available from the Drupal.org git repositories. Currently Tripal is a sandbox project while it goes through the module application process. For more information regarding the Tripal git repository including common git commands, see Tripal's Drupal.org project page.

To clone the Tripal development GIT repository, use the following command:

 git clone --recursive --branch 6.x-1.x http://git.drupal.org/sandbox/spficklin/1337878.git tripal

You can also browse the Tripal GIT repository.

Using Tripal

Full documentation on installing, configuring, and using Tripal is available from the Tripal website.

Documentation

For Developers

Tripal provides an API to help developers who wish to create new Tripal extension modules. The API provides common functions for interacting with Chado, Tripal, and for constructing or editing custom templates for a custom look-and-feel. For more information, see the following links:

• Tripal 0.6.x-0.3b API
• Tripal Developer's Handbook

Publications, Tutorials, and Presentations

Publications on or mentioning Tripal

• Tripal: a construction toolkit for online genome databases. ^[1]

Tutorials

Tutorials are available for several different versions of Tripal:

• Tripal Tutorial (v1.0) - for the latest, greatest version of Tripal
• Tripal Tutorial (v0.3.1b) - The full v0.3.1b tutorial
• Tripal Tutorial (v0.3.1b VM) - for use with the Tripal virtual machine
• Tripal Tutorial (pre version 0.3b) - from the 2010 GMOD Spring School
• Tripal Tutorial - for v0.2 - from the 2009 GMOD Summer School - Americas

Contacts and Mailing Lists

Tripal in the wild

Public installations of Tripal:

• Fagaceae Genomics Web
• Citrus Genome Database
• Pulse Crop Genomics and Breeding
• Marine Genomics Project (MG.org)
• Cacao Genome Database
• Genome Database for Vaccinium
• Cool Season Food Legume Genome Database
• Genome Database for Rosaceae
• Hardwood Genomics Project

Tripal Development

Tripal is under development at several institutions, including the Mainlab Bioinformatics at Washington Statue University, the University of Saskatchewan and the Clemson University Genomics Institute (CUGI).

More on Tripal

See Category:Tripal

1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:21959868