Transcript Brainstorming

University of Illinois at Urbana-Champaign
BeeSpace Project
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5-year NSF-funded project
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Project Goals
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Develop open bioinformatics resources
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Support functional analysis of social behavior
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Initial prototype focused on honey bee research
University of Illinois at Urbana-Champaign
What is BeeSpace?
University of Illinois at Urbana-Champaign
BeeSpace Functional Concepts
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SPACES merge, switch
MAPS topic, cluster, ontology
DOCUMENTS summarize, annotate
University of Illinois at Urbana-Champaign
What does BeeSpace do?
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Lets you search and navigate biology literature
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Conceptual navigation of semantic descriptions
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Presents diverse databases in a uniform space
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Enables hypothesis development and testing
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Goes beyond keyword search, to find functional
descriptions from biology literature
Automatic generation of gene descriptions
University of Illinois at Urbana-Champaign
BeeSpace 4.0: New Features
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Single AJAX Window with Collapsible Panes
Email Model: Folders, Lists, Messages
Coordinated Levels of Resolution
University of Illinois at Urbana-Champaign
How is BeeSpace licensed?
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Portions are GPL v2
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Remainder is subject to negotiation
University of Illinois at Urbana-Champaign
BeeSpace Development
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Small team of students and professionals
4th year of full-time development
Current version, 3.6, is available for demo
Version 4.x scheduled for late 2008 release
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New AJAX user interface using Ext JS v2.0
Switching from Java/JSF to Python/Django
University of Illinois at Urbana-Champaign
Killer App: Gene Summarizer
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“Convert genes into abstracts”
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Pass gene ID's and keywords to Summarizer
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Queries large literature DB's (250GB+)
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Returns highly relevant abstracts
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Automatically generates descriptions of genes
similar to those created by human curators
University of Illinois at Urbana-Champaign
Research Value to Biologists
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The generated summaries are directly useful to
biologists, and also serve as entry points to
enable them to quickly navigate relevant
literatures
BeeSpace live prototype:
http://beespace.uiuc.edu
University of Illinois at Urbana-Champaign
Publish BeeSpace as Web Service
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We’re committed to publishing all BeeSpace
components as web services
Gene Summarizer is first available service
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Highly interoperable across platforms
Simple integration with existing software
How simple, you ask?...
University of Illinois at Urbana-Champaign
Really Simple GMOD Integration
Change 1 line of code in “gbrowse_details”
From:
print $CONFIG->header || h1("$head_name Details");
To:
print $CONFIG->header || h1("<a
href=http://workerbee.igb.uiuc.edu:8080/BeeSpace/S
earchServlet?query=$name&cid=2293&submit=Sum
marize target=_blank>$head_name</a> Details");
University of Illinois at Urbana-Champaign
What's Next for BeeSpace?
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BeeSpace v4.0
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Streamlined AJAX web interface
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Faster searching
GMOD integration
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More BeeSpace web service functionality
University of Illinois at Urbana-Champaign
The Future: AJAX + Web Services
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AJAX consuming web services
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Example: Google Maps
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Gaining popularity in industry
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Future of BeeSpace design?
University of Illinois at Urbana-Champaign
Thank You
University of Illinois at Urbana-Champaign