What is Tripal?

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Tripal is a suite of PHP5 modules that bridges the Drupal Content Management System (CMS) and GMOD Chado. The goal is to simplify construction of a community genomics, genetics or biological website to enable individual labs or research communities to construct a high-quality, standards-based website for data sharing and collaboration.

Content Management System

Definition From Wikipedia:

A content management system (CMS) is the collection of procedures used to manage work flow in a collaborative environment. These procedures can be manual or computer-based. The procedures are designed to do the following:

  • Allow for a large number of people to contribute to and share stored data
  • Control access to data, based on user roles (defining which information users or user groups can view, edit, publish, etc.)
  • Aid in easy storage and retrieval of data
  • Reduce repetitive duplicate input
  • Improve the ease of report writing
  • Improve communication between users

In a CMS, data can be defined as nearly anything: documents, movies, pictures, phone numbers, scientific data, and so forth. CMSs are frequently used for storing, controlling, revising, semantically enriching, and publishing documentation. Serving as a central repository, the CMS increases the version level of new updates to an already existing file. Version control is one of the primary advantages of a CMS.

Drupal

Drupal is an open-source freely available CMS with thousands of users and existing sites. Features of Drupal

  • A well-supporting community.
  • Books, tutorials and on-line forums for help .
  • Hundreds of user-contributed extension modules that are freely available.
  • Hundreds of user-contributed themes to instantly change the look-and-feel of the site
  • User management infrastructure.
  • Allows for non-coding manipulation of the website contents. Anyone can edit content.
  • Easy to install and maintain

Drupal website: http://www.drupal.org Drupal modules: http://www.drupal.org/project/modules Drupal themes: http://www.drupal.org/project/themes

Tripal v2.0 is compatible with Drupal v7.

Chado

You can find more detailed information about Chado here: http://gmod.org/wiki/Chado_-_Getting_Started. However, one thing to remember in regards to Tripal organization is that Chado has a modular structure:

  • Audit - for database audits
  • Companalysis - for data from computational analysis
  • Contact - for people, groups, and organizations
  • Controlled Vocabulary (cv) - for controlled vocabularies and ontologies
  • Expression - for summaries of RNA and protein expresssion
  • General - for identifiers
  • Genetic - for genetic data and genotypes
  • Library - for descriptions of molecular libraries
  • Mage - for microarray data
  • Map - for maps without sequence
  • Organism - for taxonomic data
  • Phenotype - for phenotypic data
  • Phylogeny - for organisms and phylogenetic trees
  • Publication (pub) - for publications and references
  • Sequence - for sequences and sequence features
  • Stock - for specimens and biological collections
  • WWW -

Tripal is also modular following these same designations.

Goals of Tripal

  • Simplify Construction of Biological Databases
    • Reduce time of development
    • Reduce costs
    • Reduce technical resources (i.e. programmers, systems admins).
    • A non-technical site administrator can add content without knowing PHP, HTML, JavaScript.
  • Greater Flexibility of the Biological Website
    • Social Networking
    • Non-biological content
    • Outreach, tutorials, documentation, protocols, publications
  • Expandability
    • Site can be programmatically expanded in any way
    • Changes to base-code are not needed but modules are added.
    • Availability of an Application Programmer Interface (API)
  • Re-usability
    • All code can be shared. Expansion modules created by one group can be shared with all.

Structure of Tripal

Tripal is a collection of modules that integrate with Drupal. These modules are divided into hierarchical categories:

The Tripal Core level contains supportive functionality for all other modules. It contains

  • A jobs management utility
  • A utility to manage materialized views
  • An API for these features
  • Functions for managing module specific CV terms
  • Functions for interfacing with Chado.

The Chado-centric modules provide:

  • Edit/Update/Delete for Chado modules.
  • Bulk loaders for these data
  • Basic visualizations for data in Chado specific for the module
  • An API for easily accessing Chado.

Analysis modules provide

  • Custom visualization for specific analyses (e.g. Blast, KEGG, InterProScan, Unigene construction)
  • Uses the API from the Tripal Analysis (Chado-centric) module.

Applications:

  • These are full blown applications that use Tripal, Drupal and Chado and typically consist of several Chado-centric modules, Analysis modules and custom built modules. (e.g. Breeders Toolbox currently under construction).

Sites Running Tripal

Site Name URL
Banana Genome Hub http://banana-genome.cirad.fr/
Pulse Crops Genomics & Breeding http://knowpulse2.usask.ca/portal/
Genome Database for Vaccinium http://www.vaccinium.org
Genome Database for Rosacaee http://www.rosaceae.org
Cool Season Food Legume Database http://www.gabcsfl.org
Cacao Genome Database http://www.cacaogenomedb.org
Fagaceae Genome Web http://www.fagaceae.org
Citrus Genome Database http://www.citrusgenomedb.org
Marine Genomics Project http://www.marinegenomics.org

Resources

The Tripal home site where you can find everything about Tripal: http://tripal.info

GMOD Tripal mailing lists: http://gmod.org/wiki/GMOD_Mailing_Lists

GMOD Tutorials from previous GMOD schools: http://gmod.org/wiki/Tripal

Contributing Organizations

Individuals from these organizations have provided design and coding for Tripal v2.0

Acknowledgments are extended to the Clemson University Genomics Institute where Tripal was first conceived and where development of earlier releases was performed.

Also, special thanks are extended to the GMOD project for logistical support and community interaction!!

Funding

Funding for Tripal v2.0 has been provided through various grants from various sources.

 

Publications

  1. Lacey-Anne Sanderson, Stephen. P. Ficklin, Chun-Huai Cheng, Sook Jung, Frank A. Feltus, Kirstin E. Bett, Dorrie Main. Tripal v1.1: a Standards-based Platform for Construction of Online Genetic and Genomic Databases. Databases, Sept 2013.
  2. Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett, Dorrie Main. Tripal: a construction Toolkit for Online Genome Databases. Database, Sept 2011.