View source for WebGBrowse

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{{ImageLeft|cgb_logo.png|WebGBrowse at the Center for Genomics and Bioinformatics||http://cgb.indiana.edu/}}
[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]. 

== Documentation ==

Information on [http://webgbrowse.cgb.indiana.edu/ 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/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://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.
* [[January 2009 GMOD Meeting#WebGBrowse: GBrowse Configuration Management|"WebGBrowse: GBrowse Configuration Management"]], presentation by Ram Podicheti at the [[January 2009 GMOD Meeting]].

== WebGBrowse and GMOD ==

WebGBrowse was [http://gmod.827538.n3.nabble.com/WebGBrowse-GMOD-Nomination-td846493.html nominated] for [[GMOD Membership]] on 2010/05/26.  Feedback was universally favorable and we are now in the process of bringing WebGBrowse officially into GMOD.

== Mailing Lists ==

{{MailingListsFor|WebGBrowse}}

[[Category:External]]
[[Category:GBrowse]]
Available on platform	web +
Has URL	http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html + and http://webgbrowse.cgb.indiana.edu +
Has description	The [[GBrowse\|Generic Genome Browser (GBro … 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 public WebGBrowse server at CGB.ana.edu/ public WebGBrowse server at CGB]. +
Has development status	inactive +
Has download URL	http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html +
Has input format	GFF3 +
Has logo	WebGBrowseLogo.png +
Has output format	GBrowse configuration file +
Has software maturity status	mature +
Has support status	active +
Has topic	WebGBrowse +
Has website	http://webgbrowse.cgb.indiana.edu +
Link type	download +, source code +, website + and public server +
Release date	1 January 2009 +
Tool functionality or classification	Genome Visualization and Editing + and Tool Integration +
Written in language	Perl + 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 +