[Arabidopsis] BAR News: eFP Browser for At-TAX data sets, ePlant, and call for views

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart from utoronto.ca)
Fri Aug 21 16:37:05 EST 2009

Hello Arabidopsis Researchers,

The Bio-Array Resource is happy to announce the inclusion of At-TAX data
sets from Detlef Weigel's group/s in Tuebingen (Laubinger et al. 2008 and
Zeller et al. 2009) in our Arabidopsis eFP Browser. This inclusion is made
possible through the use of JSON-based webservices developed by Christian
Widmer and Stefan Henz, whereby the eFP Browser retrieves At-TAX data
directly from Tuebingen for display. Thanks also to Sascha Laubinger for
information regarding the samples. The inclusion of At-TAX data means that
expression information for several thousand more Arabidopsis genes not
included on the ATH1 chip is now available within the eFP Browser system.
The dual view At-TAX/ATH1 eFP view was implemented by Yuan Ji in my lab. 

The BAR is also pleased to introduce a conceptual implementation of a
"Google Earth" for plant biology, called ePlant. Try it at
bar.utoronto.ca/eplant! ePlant permits or will soon permit easy 3D viewing
of large plant biology data sets from the km to nm scale (sequence
variation, gene expression, subcellular localisation, protein interactors
and protein structure for now). ePlant was implemented by Geoff Fucile,
David Di Biase, Shokoufeh Khodabandeh and Hardeep Nahal, and makes extensive
use of data from the Arabidopsis community: Schmid et al. 2005, Geisler-Lee
et al. 2007, the SUBA database from A. Harvey Millar's lab via webservice,
and soon sequence polymorphism data from Joe Ecker and others. A new, much
faster version based on Google's O3D 3D rendering engine will be available
shortly. The ePlant system uses 3D models of the type used in the video
games and the computer generated imagery industry. We've also set up the 3D
Data Display Initiative at 3ddi.org to further these kind of developments. 

Finally, we're expanding our cell-type-specific views in the eFP Browser
with the inclusion of several new cell-type-specific data sets, such as a
floral meristem set from Venu Reddy's lab at UCR, pollen germination data
from Mark Johnson (Brown) and Ravishankar Palanivelu (Arizona), and salt and
nitrogen root cell-type-responses from the Benfey (Duke) and Birnbaum (NYU)
labs. If you're aware of any other cell-type-specific data sets, let us know
and we'll add them this Fall!

Best regards and, as always, we welcome any feedback.


Nicholas Provart, PhD
Assistant Professor, Plant Cyberinfrastructure & Systems Biology
Director, Graduate Program in Genome Biology and Bioinformatics
Member, Centre for the Analysis of Genome Evolution and Function
Rm 3051, Dept. of Cell and Systems Biology, Uni. Toronto
25 Willcocks St., Toronto, ON. M5S 3B2. CANADA

Tel. (+1) (416) 978-7141, Fax. (+1) (416) 978-5878
URL. http://www.csb.utoronto.ca/faculty/provart-nicholas
The Bio-Array Resource. http://www.BAR.utoronto.ca   
email. nicholas.provart from utoronto.ca
TTC. Spadina LRT, Willcocks St.

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