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BeeSpace Project

BeeSpace Project. 5-year NSF-funded project Project Goals Develop open bioinformatics resources Support functional analysis of social behavior Initial prototype focused on honey bee research. What is BeeSpace?. BeeSpace Functional Concepts. SPACES merge, switch

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BeeSpace Project

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  1. BeeSpace Project • 5-year NSF-funded project • Project Goals • Developopen bioinformatics resources • Support functional analysis of social behavior • Initial prototype focused on honey bee research

  2. What is BeeSpace?

  3. BeeSpace Functional Concepts • SPACES merge, switch • MAPS topic, cluster, ontology • DOCUMENTS summarize, annotate

  4. What does BeeSpace do? • Lets you search and navigate biology literature • Conceptual navigation of semantic descriptions • Presents diverse databases in a uniform space • Enables hypothesis development and testing • Goes beyond keyword search, to find functional descriptions from biology literature • Automatic generation of gene descriptions

  5. BeeSpace 4.0: New Features • Single AJAX Window with Collapsible Panes • Email Model: Folders, Lists, Messages • Coordinated Levels of Resolution

  6. How is BeeSpace licensed? • Portions are GPL v2 • Remainder is subject to negotiation

  7. BeeSpace Development • 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 • New AJAX user interface using Ext JS v2.0 • Switching from Java/JSF to Python/Django

  8. Killer App: Gene Summarizer • “Convert genes into abstracts” • Pass gene ID's and keywords to Summarizer • Queries large literature DB's (250GB+)‏ • Returns highly relevant abstracts • Automatically generates descriptions of genes similar to those created by human curators

  9. Research Value to Biologists • 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

  10. Publish BeeSpace as Web Service • We’re committed to publishing all BeeSpace components as web services • Gene Summarizer is first available service • Highly interoperable across platforms • Simple integration with existing software How simple, you ask?...

  11. Really Simple GMOD Integration Change 1 line of code in “gbrowse_details” From: print $CONFIG->header || h1("$head_name Details"); To: print $CONFIG->header || h1("<a href=http://workerbee.igb.uiuc.edu:8080/BeeSpace/SearchServlet?query=$name&cid=2293&submit=Summarize target=_blank>$head_name</a> Details");

  12. What's Next for BeeSpace? • BeeSpace v4.0 • Streamlined AJAX web interface • Faster searching • GMOD integration • More BeeSpace web service functionality

  13. The Future: AJAX + Web Services • AJAX consuming web services • Example: Google Maps • Gaining popularity in industry • Future of BeeSpace design?

  14. Thank You

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