Difference between revisions of "Tripal"

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<center>{{#icon: TripalLogo.jpg|Tripal|200|Tripal}}</center>
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{{Tool data
__NOTITLE__
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|name=Tripal
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|status=mature
 +
|dev=active
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|support=active
 +
|type=Database (Chado) web front ends, Database tools, Development Platform (has API)
 +
|platform=linux, unix, os x, web
 +
|about=Tripal is a web front end for [[Chado]] databases, based on the [http://www.drupal.org 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.
  
{{ComponentBox|{{TripalResourcesBoxItem}}
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Features and advantages of Tripal:
| | | | | |}}
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{{TocLeft}}
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Tripal is a [[Chado]] database web front end based on a collection of [http://www.drupal.org Drupal] modules.  Tripal is under development at the [http://www.genome.clemson.edu/ Clemson University Genomics Institute] (CUGI).  Tripal initially started as a web front-end for the [http://www.marinegenomics.org Marine Genomics Project (MG.org)].  Work on the interface is currently ongoing for the MG.org project as well as the [http://www.fagaceae.org/ Fagaceae Genomics Web], and other CUGI projects.  Collaborators on the project include investigators from the [http://www.hml.noaa.gov/ Hollings Marine Lab], The [http://www.musc.edu Medical University of South Carolina], the [http://www.bioinfo.wsu.edu Main Bioinformatics Laboratory] at [http://www.wsu.edu Washington State University] and Clemson's [http://citi.clemson.edu CyberInfrastructure Technology Integration] group. Tripal can be downloaded from the GMOD [[SVN]] repository or the [http://www.genome.clemson.edu/software/tripal Tripal homepage].
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== Documentation ==
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* Allows rapid development of an online genomic database.
 
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* Site administrators can add non-biological content to their sites and allow editing of content by non-technical users.
* [[Tripal Tutorial]] - from the [[2009 GMOD Summer School - Americas]]
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* Tripal User's Guide - [[Media:TripalUsersGuideJan2010.pdf|v0.2]], [[Media:TripalUsersGuideJune2009.pdf|v0.1b]]
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* [http://www.genome.clemson.edu/software/tripal Tripal project page at Clemson]
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==Advantages to Drupal==
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Drupal provides several benefits as a front-end for [[Chado]], including:
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* A content management system that allows ordinary users to provide and update content.
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* A web framework that provides a simplified API for creating online forms, pages, content blocks, etc.
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* Free, it's open-source!
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* Large community, active development, and well documented.
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* A large collection of publicly available modules that instantly enhance a site and reduce development time.
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* Includes an infrastructure for managing user and data access permissions.
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* Built-in and extendable full-text searching capability.
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* Highly customizable:
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** Users add content in an easy intuitive manner.
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** Web designers create a custom "look-and-feel" for their Drupal sites.
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** Programmers develop new modules for new content types and functionality.
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* Provides social-networking functionality such as commenting, social bookmarking, etc.
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==Advantages to Tripal==
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Upon initial release, Tripal will provide several benefits:
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* Quick development of an online genomic database.
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* Integrates directly with GMOD [[Chado]].
 
* Integrates directly with GMOD [[Chado]].
* Provides visualizations for chado "modules" such as [[Chado Sequence Module|features]], [[Chado Companalysis Module|analyses]], [[Chado Library Module|libraries]], [[Chado Modules|etc]].
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* Provides visualizations for Chado "modules" such as [[Chado Sequence Module|features]], [[Chado Companalysis Module|analyses]], [[Chado Library Module|libraries]], [[Chado Stock Module|stocks]], [[Chado Modules|and others]].
 
* Provides an interface for easy editing/updating of data in Chado.
 
* Provides an interface for easy editing/updating of data in Chado.
 
* Provides full text and categorical search capabilities for Chado content.
 
* Provides full text and categorical search capabilities for Chado content.
 
* Can integrate GMOD tools such as [[CMap]] and [[GBrowse]].
 
* Can integrate GMOD tools such as [[CMap]] and [[GBrowse]].
 +
* Integrates with powerful Drupal features like [http://drupal.org/project/views Drupal views] and [http://drupal.org/project/panels 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)
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* Loaders for GFF3 and FASTA format files.
 +
* Provides an API to allow for creation of custom extensions by anyone.
  
==Future aspirations for Tripal==
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What is Tripal capable of? Check out the [http://tripal.gmod.oicr.on.ca/1.1/ Tripal demo server].
* Web-based [[Chado]] installation.
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* Built-in data management utilities for bulk load of data.
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* A workflow infrastructure for online data analysis through online tools.
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* integration with high-performance/high-throughput computational resources.
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== Support ==
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Questions on Tripal can be posted to the mailing list.
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{{MailingListsFor|Tripal}}
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{{ImageRight|Cugi_logo6.5.jpg|CUGI|200|http://www.genome.clemson.edu/}}
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Tripal was developed and is maintained by [http://www.genome.clemson.edu/ Clemson University Genomics Institute (CUGI)].  Tripal development is led by [[User:Sficklin|Stephen Ficklin]].  CUGI also offers custom Tripal development (and premium support) on a fee basis.  Contact [[User:Sficklin|Stephen Ficklin]] for more information.
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==== Tripal Homepage ====
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Get the most up-to-date information about Tripal [http://www.tripal.info here].
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|open source=Yes
 +
|licence=GPLv2
 +
|input=[[GFF3]], FASTA, Chado DB, tab-separated data, OBO ontology files
 +
|language=PHP, Javascript, HTML
 +
|use template=Yes
 +
|logo=TripalLogo.png
 +
|contact=spficklin@gmail.com
 +
|mail={{MailingListsFor|Tripal}}
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|dl src=The latest development version of Tripal is available at the [https://github.com/tripal/tripal Tripal GitHub Page]
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|tutorials=[http://tripal.info/tutorials/v2.x Tripal 2.x User's Guide]
 +
|getting started preamble=Full documentation on installing, configuring, and using Tripal is available from the [http://tripal.info/ Tripal website].
 +
}}
 
[[Category:Chado]]
 
[[Category:Chado]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]
 
[[Category:Tripal]]
 
[[Category:Tripal]]
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{{SemanticLink
 +
|linkurl=http://tripal.info
 +
|linktitle=Tripal Home
 +
|linktype=home page
 +
}}
 +
{{SemanticLink
 +
|linkurl=http://tripal.info/tutorials/v2.x/installation
 +
|linktitle=Download and Install Tripal
 +
|linktype=download
 +
}}
 +
{{InteroperableComponent
 +
|relationship=can embed
 +
|object=GBrowse
 +
}}
 +
{{InteroperableComponent
 +
|relationship=can embed
 +
|object=CMap
 +
}}
 +
{{InteroperableComponent
 +
|relationship=can embed
 +
|object=Galaxy
 +
}}
 +
{{InteroperableComponent
 +
|relationship=provides interface for
 +
|object=Chado
 +
}}

Latest revision as of 16:33, 29 June 2016

Tripal logo
Status
  • Mature release
  • Development: active
  • Support: active
Licence
{{{PAGENAME}}} is open source

GPLv2

Resources
Interoperable Components


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.

What is Tripal capable of? Check out the Tripal demo server.

Tripal Homepage

Get the most up-to-date information about Tripal here.



Downloads

The latest development version of Tripal is available at the Tripal GitHub Page


Using Tripal

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



Publications, Tutorials, and Presentations

Tutorials

Tripal 2.x User's Guide


Contacts and Mailing Lists

Mailing List Link Description Archive(s)
Tripal gmod-tripal Tripal-related announcements, questions, and requests for help from developers and the community. Nabble (2010/05+), Sourceforge
gmod-tripal-devel Tripal development list Nabble, Sourceforge




More on Tripal

See Category:Tripal



"home page" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property. "home page" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property. "home page" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property. "home page" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property. "home page" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property. "home page" is not in the list of possible values (website, download, source code, public server, demo server, wild URL, documentation, publication, social media, other) for this property.

Facts about "Tripal"RDF feed
Available on platformlinux +, unix +, os x + and web +
Has URLhttp://tripal.info + and http://tripal.info/tutorials/v2.x/installation +
Has descriptionTripal is a web front end for Chado daTripal 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.

What is Tripal capable of? Check out the Tripal demo server.

Tripal Homepage[edit]

Get the most up-to-date information about Tripal here.
bout Tripal here. +
Has development statusactive +
Has input formatGFF3 +, FASTA +, Chado DB +, tab-separated data + and OBO ontology files +
Has licenceGPLv2 +
Has logoTripalLogo.png +
Has software maturity statusmature +
Has support statusactive +
Has titleTripal Home + and Download and Install Tripal +
Has topicTripal +
Interaction typecan embed + and provides interface for +
InteractorTripal +
Interacts withGBrowse +, CMap +, Galaxy + and Chado +
Is open sourceYes +
Link typedownload +
Tool functionality or classificationDatabase (Chado) web front ends +, Database tools + and Development Platform (has API) +
Written in languagePHP +, Javascript + and HTML +
Has subobjectThis property is a special property in this wiki.Tripal#http://tripal.info +, Tripal#http://tripal.info/tutorials/v2.x/installation +, Tripal +, Tripal +, Tripal + and Tripal +