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@@ -2,22 +2,23 @@ What is Tripal?
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--------------
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Tripal is a collection of open-source freely available Drupal modules
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and is a member of the GMOD family of tools. Tripal serves as a web
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-interface for the GMOD Chado database and is designed to allow anyone
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-with genomic data to quickly create an online genomic database using
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-community supported tools.
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+interface for the GMOD Chado database and is designed to reduce the
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+time and cost required for construction of an online genomic, genetic
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+and breeding database.
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Features
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--------------
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- a Chado installer
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- Data loaders for ontologies (controlled vocabularies), GFF files,
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- and FASTA files
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- - Generic Data Loader Modules allows for creation of custom loading
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- templates
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+ and FASTA files, publications (from PubMed and AGIRCOLA).
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+ - Generic Bulk Data Loader Modules allows for creation of custom
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+ loading templates.
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- Drupal nodes (web pages) are automatically generated for organisms,
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genomic features, biological libraries, and stocks
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- - Web pages can be enriched with analysis results from BLAST,
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- KAAS/KEGG, InterProScan, and Gene Ontology (GO)
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+ - Supports creation of materialized views for faster data queries.
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+ - Display templates are provided for all content types for
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+ easier customization.
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- Views Integration allows for custom listings of data
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- Content pieces exposed as blocks allowing the use of Panels for
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custom layouts of Tripal Nodes
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@@ -25,25 +26,19 @@ Features
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Required Modules
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--------------
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- - Drupal 6.x (work is currently underway for a 7.x compatible
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- version)
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- - Drupal Core Modules: Search and Path
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+ - Drupal 7.x
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+ - Drupal Core Modules: Search, Path and PHP modules.
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+ - Drupal contributed modules: Views
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- Database containing GMOD Chado Schema (can be installed by the
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Tripal Core module)
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NOTE: A PostgreSQL database is required for installation of the
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Chado Schema
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-Highly Recommended Modules
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- - Views 2.x (Views 3.x compatible version already exists in 6.x-0.4-dev)
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- - Views Data Export
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-
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-
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Installation
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Please follow the online tutorial for installation instructions:
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http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
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-
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Customization
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--------------
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Tripal can be used “as is” but also allows for complete customization.
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@@ -51,21 +46,3 @@ PHP-based template files are provided for all data types to allow for
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precise customizations as required by the community. A well-developed
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Tripal API provides a uniform set of variables and functions for
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accessing any and all data within the Chado database.
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-
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-
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-Future Work
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---------------
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-Currently, Tripal only supports a large subset of the
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-current Chado schema, but further development is underway. Meanwhile,
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-others can use the Tripal API to develop their own extensions. Those
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-extensions can in turn be made available for anyone to use. These
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-custom extensions, the Tripal package, and access to support resource
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-such as an active mailing list can be found on the Tripal website
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-(http://tripal.sourceforge.net).
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-
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-For more information, see the recent publication:
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-
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-Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret
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-Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett, Dorrie
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-Main. Tripal: a construction Toolkit for Online Genome Databases.
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-Database, Sept 2011. Vol 2011.
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Stephen Ficklin