Difference between revisions of "WebGBrowse"

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{{Tool data
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|name=WebGBrowse
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|status=mature
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|dev=inactive
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|support=active
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|type=Genome Visualization and Editing, Tool Integration
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|platform=web
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|about=The [[GBrowse|Generic Genome Browser (GBrowse)]] is one of the most widely used visualization tools for sequence display characterized by a rich set of utilities helpful in presenting a variety of genome features pertaining to a reference sequence. Despite the tool being meant for easy use by the biologists, the administration of GBrowse can become tedious, particularly for those without adequate computational resources. Moreover, there is no exhaustive, accurate, "GBrowse user's perspective" based reference available for the various glyphs useful in building the feature tracks on GBrowse, thus adding to the complexities involved in configuration.
  
[[Image:WebGBrowseLogo.png|500px|center]]
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WebGBrowse guides the users through the process of configuring the [[GFF3]] datasets for GBrowse display. It presents the user with a "Glyph Library" comprising of around 40 different glyphs to choose from. It generates the configuration data by collecting the user's input through an organized, step-by-step process guided by the configurable parameter information available in the glyph library. A summary information on all the available glyphs can be viewed at the glyph library page. A pre-installed GBrowse instance allows the users to preview/load their datasets with desired configuration in GBrowse without requiring them to prepare any computer hardware, install any software or learn sophisticated GBrowse configuration rules for feature display.
  
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In other words, WebGBrowse addresses most of the intricacies involved in GBrowse administration, so that even a computer non-savvy biologist can configure his GFF dataset without worrying about GBrowse software installation or GBrowse configuration semantics.
  
{{ComponentBox
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WebGBrowse can be [http://webgbrowse.cgb.indiana.edu/software.html downloaded] and installed locally, or you can use the [http://webgbrowse.cgb.indiana.edu/ public WebGBrowse server at CGB].
|{{WebGBrowseResourcesBoxItem}}
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|input=[[GFF3]]
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|output=GBrowse configuration file
 
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|language=Perl, GBrowse config file
[[File:cgb_logo.png|link=http://cgb.indiana.edu/|right|WebGBrowse at the Center for Genomics and Bioinformatics]]
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|release date=2009/01/01
 
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|logo=WebGBrowseLogo.png
[http://webgbrowse.cgb.indiana.edu/ WebGBrowse] is a web interface for setting up [[GBrowse]] instances. It helps both biologists and bioinformaticians by allowing them to upload genome annotation information in [[GFF3]] format, configure display of each genomic feature through simple mouse clicks on a web browser and visualize the configured genome with the integrated GBrowse software. Thus, for biologists, WebGBrowse relieves both the burden of installing GBrowse and the need to learn the configuration semantics in order to setup their data on GBrowse. For bioinformaticians who are new to [[GBrowse]], WebGBrowse offers a headstart into understanding [http://webgbrowse.cgb.indiana.edu/glyphdoc.html GBrowse glyphs] and learning how to configure them. WebGBrowse is a good match for any organization that has users who want to create their own GBrowse instances, but lack enough computing resources and expertise to do so. WebGBrowse was developed at [http://www.iub.edu/ Indiana University's] [http://cgb.indiana.edu/ Center for Genomics and Bioinformatics]. WebGBrowse can be [http://webgbrowse.cgb.indiana.edu/software.html downloaded] and installed locally, or you can use the [http://webgbrowse.cgb.indiana.edu/ WebGBrowse at CGB].
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|screenshot=[[File:WebGBrowseAddTrack.jpg|300px|none|thumb|''Add new track'' dialog in WebGBrowse]]
 
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|mail={{MailingListsFor|WebGBrowse}}
 
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|dl src=Latest release from [http://webgbrowse.cgb.indiana.edu/software.html CGB] or latest development version from {{SF SVN|WebGBrowse/|SourceForge}}.
[[File:WebGBrowseAddTrack.jpg|300px|none|thumb|''Add new track'' dialog in WebGBrowse]]
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|papers=http://www.ncbi.nlm.nih.gov/pubmed/19357095
 
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http://www.ncbi.nlm.nih.gov/pubmed/20194461
== Resources ==
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http://www.ncbi.nlm.nih.gov/pubmed/21400697
 
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|tutorials=;[http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html WebGBrowse Tutorial]
Information on [http://webgbrowse.cgb.indiana.edu/ WebGBrowse] is available in several places:
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:An extensive user guide and tutorial
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|doc=Information on WebGBrowse is available in several places:
 
* [http://webgbrowse.cgb.indiana.edu/tutorial.html User Tutorial] - this is an extensive user guide for WebGBrowse
 
* [http://webgbrowse.cgb.indiana.edu/tutorial.html User Tutorial] - this is an extensive user guide for WebGBrowse
 
* [http://webgbrowse.cgb.indiana.edu/glyphdoc.html GBrowse Glyph Library] - shows what all those [[GBrowse]] glyphs look like.
 
* [http://webgbrowse.cgb.indiana.edu/glyphdoc.html GBrowse Glyph Library] - shows what all those [[GBrowse]] glyphs look like.
 
* [http://webgbrowse.cgb.indiana.edu/faq.html FAQ] - Frequently asked questions for WebGBrowse.
 
* [http://webgbrowse.cgb.indiana.edu/faq.html FAQ] - Frequently asked questions for WebGBrowse.
* Download source - Latest release from [http://webgbrowse.cgb.indiana.edu/software.html CGB] or latest development version from {{SF SVN|WebGBrowse/|SourceForge}}.
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|gmod date=2010
* [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/12/1550 "Podicheti R., Gollapudi R., Dong Q. (2009). WebGBrowse - a web server for GBrowse."] ''Bioinformatics'' 25(12): 1550-1551. - the WebGBrowse paper.
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|survey link=
* [[January 2009 GMOD Meeting#WebGBrowse: GBrowse Configuration Management|"WebGBrowse: GBrowse Configuration Management"]], presentation by Ram Podicheti at the [[January 2009 GMOD Meeting]].
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|contact email=[mnrusimh@indiana.edu Ram Podicheti]
 
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|integration=
== Mailing Lists ==
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|dev status=
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}}
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<!-- To change the contents of this page, please go to http://gmod.org/wiki/WebGBrowse/tool_data -->
  
{{MailingListsFor|WebGBrowse}}
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{{ :WebGBrowse/tool_data | template = Template:ToolDisplay }}
  
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]
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{{SemanticLink
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|linkurl=http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html
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|linktype=download
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}}
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{{SemanticLink
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|linkurl=http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html
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|linktype=source code
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}}
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{{SemanticLink
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|linkurl=http://webgbrowse.cgb.indiana.edu
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|linktype=website
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}}
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{{SemanticLink
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|linkurl=http://webgbrowse.cgb.indiana.edu
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|linktype=public server
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}}

Latest revision as of 21:26, 16 October 2013

WebGBrowse logo
Status
  • Mature release
  • Development: inactive
  • Support: active
Resources


About WebGBrowse

The Generic Genome Browser (GBrowse) is one of the most widely used visualization tools for sequence display characterized by a rich set of utilities helpful in presenting a variety of genome features pertaining to a reference sequence. Despite the tool being meant for easy use by the biologists, the administration of GBrowse can become tedious, particularly for those without adequate computational resources. Moreover, there is no exhaustive, accurate, "GBrowse user's perspective" based reference available for the various glyphs useful in building the feature tracks on GBrowse, thus adding to the complexities involved in configuration.

WebGBrowse guides the users through the process of configuring the GFF3 datasets for GBrowse display. It presents the user with a "Glyph Library" comprising of around 40 different glyphs to choose from. It generates the configuration data by collecting the user's input through an organized, step-by-step process guided by the configurable parameter information available in the glyph library. A summary information on all the available glyphs can be viewed at the glyph library page. A pre-installed GBrowse instance allows the users to preview/load their datasets with desired configuration in GBrowse without requiring them to prepare any computer hardware, install any software or learn sophisticated GBrowse configuration rules for feature display.

In other words, WebGBrowse addresses most of the intricacies involved in GBrowse administration, so that even a computer non-savvy biologist can configure his GFF dataset without worrying about GBrowse software installation or GBrowse configuration semantics.

WebGBrowse can be downloaded and installed locally, or you can use the WebGBrowse at CGB.

Visit the WebGBrowse website.

Screenshots

Add new track dialog in WebGBrowse

Downloads



Using WebGBrowse

Documentation

Information on WebGBrowse is available in several places:

Publications, Tutorials, and Presentations

Publications on or mentioning WebGBrowse

PMID:19357095

Tutorials

WebGBrowse Tutorial
An extensive user guide and tutorial


Contacts and Mailing Lists

Mailing List Link Description Archive(s)
WebGBrowse gmod-webgbrowse Questions, announcements, and development postings about the WebGBrowse front end to GBrowse configuration. Nabble, Sourceforge


WebGBrowse Development

Development team

WebGBrowse at the Center for Genomics and Bioinformatics
WebGBrowse was developed at Indiana University's Center for Genomics and Bioinformatics.


More on WebGBrowse


Raw tool data at WebGBrowse/tool data

Facts about "WebGBrowse"RDF feed
Available on platformweb +
Has URLhttp://webgbrowse.cgb.indiana.edu/webgbrowse/software.html + and http://webgbrowse.cgb.indiana.edu +
Has descriptionThe [[GBrowse|Generic Genome Browser (GBroThe Generic Genome Browser (GBrowse) is one of the most widely used visualization tools for sequence display characterized by a rich set of utilities helpful in presenting a variety of genome features pertaining to a reference sequence. Despite the tool being meant for easy use by the biologists, the administration of GBrowse can become tedious, particularly for those without adequate computational resources. Moreover, there is no exhaustive, accurate, "GBrowse user's perspective" based reference available for the various glyphs useful in building the feature tracks on GBrowse, thus adding to the complexities involved in configuration.

WebGBrowse guides the users through the process of configuring the GFF3 datasets for GBrowse display. It presents the user with a "Glyph Library" comprising of around 40 different glyphs to choose from. It generates the configuration data by collecting the user's input through an organized, step-by-step process guided by the configurable parameter information available in the glyph library. A summary information on all the available glyphs can be viewed at the glyph library page. A pre-installed GBrowse instance allows the users to preview/load their datasets with desired configuration in GBrowse without requiring them to prepare any computer hardware, install any software or learn sophisticated GBrowse configuration rules for feature display.

In other words, WebGBrowse addresses most of the intricacies involved in GBrowse administration, so that even a computer non-savvy biologist can configure his GFF dataset without worrying about GBrowse software installation or GBrowse configuration semantics.

WebGBrowse can be downloaded and installed locally, or you can use the public WebGBrowse server at CGB.
ana.edu/ public WebGBrowse server at CGB]. +
Has development statusinactive +
Has download URLhttp://webgbrowse.cgb.indiana.edu/webgbrowse/software.html +
Has input formatGFF3 +
Has logoWebGBrowseLogo.png +
Has output formatGBrowse configuration file +
Has software maturity statusmature +
Has support statusactive +
Has topicWebGBrowse +
Has websitehttp://webgbrowse.cgb.indiana.edu +
Link typedownload +, source code +, website + and public server +
Release date1 January 2009 +
Tool functionality or classificationGenome Visualization and Editing + and Tool Integration +
Written in languagePerl + and GBrowse config file +
Has subobjectThis property is a special property in this wiki.WebGBrowse#http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html + and WebGBrowse#http://webgbrowse.cgb.indiana.edu +