Brainstorming - BeeSpace - University of Illinois at Urbana-Champaign

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14 Δεκ 2013 (πριν από 3 χρόνια και 9 μήνες)

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University of Illinois at Urbana
-
Champaign


University of Illinois at Urbana
-
Champaign

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


University of Illinois at Urbana
-
Champaign

What is BeeSpace?


University of Illinois at Urbana
-
Champaign

BeeSpace Functional Concepts


SPACES

merge, switch


MAPS

topic, cluster, ontology


DOCUMENTS

summarize, annotate


University of Illinois at Urbana
-
Champaign

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 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?


Portions are GPL v2


Remainder is subject to negotiation


University of Illinois at Urbana
-
Champaign

BeeSpace Development


Small team of students and professionals


4
th

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


“Convert genes into abstracts”


Pass gene ID's and keywords to Summarizer


Queries large literature DB's (
250
GB+)



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 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 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?...


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?


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 Services


AJAX consuming web services


Example: Google Maps


Gaining popularity in industry


Future of BeeSpace design?


University of Illinois at Urbana
-
Champaign

Thank You