Edit Tool data: WebGBrowse

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The Basics[edit]

Name:
Full name	if name is an abbreviation, acronym, etc.
Status:
Current development:
Support status:
Tool classification or features:	Genome Visualization and Editing, Tool Integration
Platform:	If the tool linux unix os x windows web vm cloud
Brief description:	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. 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 [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].
Open source:
Software licence:
Type of input data	e.g. genomic sequence; taxonomic group; protein identifier; anatomy ontology, etc.
Input formats:	[[GFF3]]
Output formats:	GBrowse configuration file
Programming language(s)
Intended usage
First public release
Use standard tool display template?	yes

Files[edit]

Logo (file name)	enter the name of the file on the GMOD wiki, e.g. CoolAppLogo.png WebGBrowseLogo.png
Screenshot(s)

Contact details[edit]

Contact email
Mailing list(s)

Links[edit]

The majority of links related to the tool should be added using the interface at the bottom of the page.

Download text	If there is not a simple download URL for downloading the tool, please enter download instructions here. Download URLs can be entered in the 'Links' section below.
Download source code text	If there is not a simple download URL for downloading the source code for the tool, please enter download instructions here. URLs can be entered in the 'Links' section below. Latest release from [http://webgbrowse.cgb.indiana.edu/software.html CGB] or latest development version from {{SF SVN\|WebGBrowse/\|SourceForge}}.

Materials[edit]

Publications	http://www.ncbi.nlm.nih.gov/pubmed/19357095 http://www.ncbi.nlm.nih.gov/pubmed/20194461 http://www.ncbi.nlm.nih.gov/pubmed/21400697
Presentations
Tutorials	;[http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html WebGBrowse Tutorial] :An extensive user guide and tutorial

Extra Textual Goodies[edit]

Any introductory text for users
Software prerequisites
Installation
Configuration
Documentation	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/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.
Development team
Development status
Download/usage tracking
Logo info
See also	Any extra information, links, etc.
Extra items for component box

Free text:

{{ :WebGBrowse/tool_data | template = Template:ToolDisplay }} [[Category:GBrowse]] [[Category:GMOD Components]]

Links

URL

Title

Link type (e.g. download; tutorial; demo)

Description

URL

Title

Link type (e.g. download; tutorial; demo)

Description

URL

Title

Link type (e.g. download; tutorial; demo)

Description

URL

Title

Link type (e.g. download; tutorial; demo)

Description

Interoperable components

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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 +

Edit Tool data: WebGBrowse

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The Basics[edit]

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Materials[edit]

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