WebGBrowse A Web Server for GBrowse Configuration
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Transcript of WebGBrowse A Web Server for GBrowse Configuration
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WebGBrowse A Web Server for GBrowse Configuration
Ram Podicheti B.V.Sc. & A.H. (D.V.M.), M.S.
Staff Scientist – BioinformaticsCenter for Genomics and BioinformaticsIndiana University
01/16/2009GMOD Conference 2009San Diego CA
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Generic Genome Browser
• Most popular web based genome browser• Visualize genome features along a reference
sequence• Open Source• Highly customizable• Excellent usability• Rich set of “glyphs”
– Genome features– Quantitative Data– Sequence Alignments
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Scope of GBrowse Usage
Large Scale databases such as Community databases, Model organism databases
Lower sequencing costs
In-house sequencing and data maintenance by molecular biology labs and researchers
Current Research Trends
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Scope of GBrowse Usage
Large Scale databases such as Community databases, Model organism databases
More specific, but smaller databases such as a lab owned database or Individual Researcher’s database
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GBrowse Setup
• Software installation and maintenance
• GFF3 dataset preparation
• Writing the configuration file
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GBrowse Setup
• Software installation and maintenance
• GFF3 dataset preparation
• Writing the configuration filePerspectiv
e
Perspective
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Goal
Make GBrowse Available to Biologists without– installation hassles– worries about GBrowse configuration
semantics
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WebGBrowse
• Allows users to upload their GFF3 datasets
• Powered by a Glyph Library• Configuration information for 40+ glyphs• Assists in Configuring the display of each
genomic feature into individual tracks• Hosts the datasets with the specified
configuration settings on an integrated GBrowse server
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WebGBrowse Input
Upload the GFF3 dataset
Provide Email Address (optional)
Upload the dataset
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Configuration Panel
Unique Feature set Identified from the uploaded dataset
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Configuration Panel
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Configuration Panel
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Configuration Panel
Unique Feature set Identified from the uploaded dataset
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Configuration Panel
Unique Feature set Identified from the uploaded dataset
List of glyphs suppliedby the glyph library
Brief description of the selected glyph
A Sample Image of the selected glyph
Add Track Button
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Glyph Parameters Form
Parameter Description
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Configured Tracks shown in the configuration panel
List of tracks added so far
Configuration for the selected track
Edit Track Button
Delete Track Button
Button to displayconfigured tracksin GBrowse
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GBrowse Display with WebGBrowse Control Panel
WebGBrowse Control Panel
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Architecture
• Data Driven
• Glyph Library
• Configuration information– Initialize a data structure compatible with
HTML::FormEngine– Load into the data structure– Serialize into a YAML file (http://www.yaml.org
/)
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Important resources on the website
• Glyph Library
• Tutorial
• Software
• FAQ
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To Do List
• Expand the glyph library• Allow uploading of a pre-existing conf file and
start from there• Provide "General Section" configuration
(optional)• Add more features (Balloons, plugins etc.)• Categorizing the glyphs• Tutorial on how to add new glyphs• Callbacks?• Suggestions from GMOD group
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References
Karolchik, D. et al. (2003) The UCSC Genome Browser Database, Nucleic Acids Res, 31, 51-54.
Schlueter, S.D. et al. (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features, Genome Biol, 7, R111.
Stalker, J. et al. (2004) The Ensembl Web site: mechanics of a genome browser, Genome Res, 14, 951-955.
Stein, L.D. et al. (2002) The generic genome browser: a building block for a model organism system database, Genome Res, 12, 1599-1610.
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Acknowledgements
Rajesh GollapudiGraduate StudentSchool of InformaticsIndiana University
Dr. Qunfeng DongDirector BioinformaticsCenter for Genomics and BioinformaticsIndiana University
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Acknowledgements
Chris HemmerichStaff Scientist & Database Unit LeaderCenter for Genomics and BioinformaticsIndiana University
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Acknowledgements
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Acknowledgements
This research was supported in part by the Indiana METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc.
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