University of Illinois at Urbana-Champaign

University of Illinois at Urbana-Champaign

BeeSpace ProjectBeeSpace 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

University of Illinois at Urbana-Champaign

What is BeeSpace?What is BeeSpace?

University of Illinois at Urbana-Champaign

BeeSpace Functional BeeSpace Functional ConceptsConcepts

SPACES merge, switch MAPS topic, cluster, ontology DOCUMENTS summarize, annotate

University of Illinois at Urbana-Champaign

What does BeeSpace do?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

University of Illinois at Urbana-Champaign

BeeSpace 4.0: New FeaturesBeeSpace 4.0: New Features 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?How is BeeSpace licensed? Portions are GPL v2 Remainder is subject to negotiation

University of Illinois at Urbana-Champaign

BeeSpace DevelopmentBeeSpace 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

University of Illinois at Urbana-Champaign

Killer App: Gene Summarizer 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

University of Illinois at Urbana-Champaign

Research Value to BiologistsResearch 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

University of Illinois at Urbana-Champaign

Publish BeeSpace as Web Publish BeeSpace as Web ServiceService

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?...

University of Illinois at Urbana-Champaign

Really Simple GMOD Really Simple GMOD IntegrationIntegration

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");

University of Illinois at Urbana-Champaign

What's Next for BeeSpace?What's Next for BeeSpace? BeeSpace v4.0

Streamlined AJAX web interface Faster searching

GMOD integration More BeeSpace web service functionality

University of Illinois at Urbana-Champaign

The Future: AJAX + Web The Future: AJAX + Web ServicesServices

AJAX consuming web services Example: Google Maps

Gaining popularity in industry Future of BeeSpace design?

University of Illinois at Urbana-Champaign

Thank YouThank You