Difference between revisions of "Tripal"

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__NOTITLE__
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{{Tool data
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|name=Tripal
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[[File:TripalLogo.jpg|center|400px|alt=Tripal logo]]
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|status=mature
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|dev=active
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<div class="componentBox">
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|support=active
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<div class="compBoxHdr">Status</div>
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|type=Database (Chado) web front ends, Database tools, Development Platform (has API)
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*Mature release
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|platform=linux, unix, os x, web
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*active development
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|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.
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*active support
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<div class="compBoxHdr">Resources</div>
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*[http://tripal.sourceforge.net/ Home page]
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*[http://tripal.sourceforge.net/?q=download Download]
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*[http://gmod.org/extras/2008GMODCommunitySurvey.html#{{{Tripal}}} 2008 Survey]
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<div class="compBoxHdr">Events</div>
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{{SchoolBoxItem|Tripal}}
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</div>
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==About Tripal==
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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.
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Features and advantages of Tripal:
 
Features and advantages of Tripal:
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* Loaders for GFF3 and FASTA format files.
 
* Loaders for GFF3 and FASTA format files.
 
* Provides an API to allow for creation of custom extensions by anyone.
 
* Provides an API to allow for creation of custom extensions by anyone.
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Visit the [http://tripal.sourceforge.net/ Tripal website].
 
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==Downloads==
 
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Download Tripal: [http://tripal.sourceforge.net/?q=download http://tripal.sourceforge.net/?q=download]
 
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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 [http://drupal.org/node/1337878/git-instructions/6.x-1.x Tripal's Drupal.org project page].
 
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To clone the Tripal development GIT repository, use the following command:
 
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  git clone --recursive --branch 6.x-1.x http://git.drupal.org/sandbox/spficklin/1337878.git tripal
 
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You can also [http://drupalcode.org/sandbox/spficklin/1337878.git browse the Tripal GIT repository].
 
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==Using Tripal==
 
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Full documentation on installing, configuring, and using Tripal is available from the [http://tripal.sourceforge.net/?q=documentation Tripal website].
 
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===Documentation===
 
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==== For Developers ====
 
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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:
 
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* [http://tripal.sourceforge.net/docs/tripal-0.6x-0.3b/index.html Tripal 0.6.x-0.3b API]
 
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* [[Tripal Developer's Handbook]]
 
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==Publications, Tutorials, and Presentations==
 
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===Publications on or mentioning Tripal===
 
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* [[Tripal]]: a construction toolkit for online genome databases. <ref name=PMID:21959868/>
 
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===Tutorials===
 
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Tutorials are available for several different versions of Tripal:
 
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* [[Tripal Tutorial (v1.0)]] - Under construction
 
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* [[Tripal Tutorial (v0.3.1b)]] - The full v0.3.1b tutorial
 
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* [[Tripal Tutorial (v0.3.1b VM)]] - for use with the Tripal virtual machine
 
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* [[Tripal Tutorial (pre version 0.3b)]] - from the 2010 GMOD Spring School
 
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* [[Tripal Tutorial]] - for v0.2 - from the [[2009 GMOD Summer School - Americas]]
 
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==Contacts and Mailing Lists==
 
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{| class="wikitable"
 
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|
 
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! Mailing List Link
 
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! Description
 
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! Archive(s)
 
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[[:Template:MailingListsTripal]]
 
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|}
 
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==Tripal in the wild==
 
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Public installations of Tripal:
 
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*[http://www.fagaceae.org Fagaceae Genomics Web]
 
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*[http://www.citrusgenomedb.org/ Citrus Genome Database]
 
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*[http://knowpulse2.usask.ca/portal Pulse Crop Genomics and Breeding]
 
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*[http://www.marinegenomics.org/ Marine Genomics Project (MG.org)]
 
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*[http://www.cacaogenomedb.org/ Cacao Genome Database]
 
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*[http://www.vaccinium.org/ Genome Database for Vaccinium]
 
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*[http://www.gabcsfl.org/ Cool Season Food Legume Genome Database]
 
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*[http://www.rosaceae.org/ Genome Database for Rosaceae]
 
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*[http://www.hardwoodgenomics.org Hardwood Genomics Project]
 
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==Tripal Development==
 
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Tripal is under development at several institutions, including [http://www.bioinfo.wsu.edu the Mainlab Bioinformatics] at [http://www.wsu.edu Washington Statue University], the [http://www.usask.ca/ University of Saskatchewan] and the [http://www.genome.clemson.edu/ Clemson University Genomics Institute] (CUGI).
 
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==More on Tripal==
 
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See [[:Category:Tripal]]
 
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<references />
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What is Tripal capable of? Check out the [http://tripal.gmod.oicr.on.ca/1.1/ Tripal demo server].
  
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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
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|input=[[GFF3]], FASTA, Chado DB, tab-separated data, OBO ontology files
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|language=PHP, Javascript, HTML
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|use template=Yes
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|logo=TripalLogo.png
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|contact=spficklin@gmail.com
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|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]
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|getting started preamble=Full documentation on installing, configuring, and using Tripal is available from the [http://tripal.info/ Tripal website].
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}}
 
[[Category:Chado]]
 
[[Category:Chado]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]
 
[[Category:Tripal]]
 
[[Category:Tripal]]
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{{SemanticLink
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|linkurl=http://tripal.info
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|linktitle=Tripal Home
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|linktype=home page
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}}
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{{SemanticLink
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|linkurl=http://tripal.info/tutorials/v2.x/installation
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|linktitle=Download and Install Tripal
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|linktype=download
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}}
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{{InteroperableComponent
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|relationship=can embed
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|object=GBrowse
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}}
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{{InteroperableComponent
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|relationship=can embed
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|object=CMap
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}}
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{{InteroperableComponent
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|relationship=can embed
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|object=Galaxy
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}}
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{{InteroperableComponent
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|relationship=provides interface for
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|object=Chado
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}}

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.

Retrieved from "http://gmod.org/mediawiki/index.php?title=Tripal&oldid=27192"
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 da … 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[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 +