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[Arabidopsis] Araport Newsletter - Winter 2015

Krishnakumar, Vivek via arab-gen%40net.bio.net (by vKrishna from jcvi.org)
Thu Dec 24 12:47:06 EST 2015


Greetings Arabidopsis and plant researchers!

We are pleased to announce a new ThaleMine 1.8.0. data release, which now includes Arabidopsis germplasm stocks linked to the corresponding locus identifiers, and the latest genome annotation Araport11.

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** What's new in ThaleMine ** (https://apps.araport.org/thalemine/)

	* In addition to providing Gene Report pages and Gene List Enrichment analysis, you can now also conveniently connect to germplasms and stock centers for your genes/alleles of interest.

	* The most up-to-date genome annotation Araport11 Pre-Release 3 (Dec 2015) has been submitted to NCBI for final reviews.  Araport11 is available via ThaleMine and additional Araport components below.

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** About Araport ** (https://www.araport.org)

Araport aims to provide Arabidopsis and plant scientists direct access to a new generation web-based data platform. In a nutshell, users can browse and analyze a wide array of data through Araport, and can also publish their own modules for sharing data with the community or building analysis workflows. Araport has also assumed the responsibility for updating and revising genome annotation (Araport11) and the reference genome sequence.

Features include:

	* ThaleMine (https://apps.araport.org/thalemine/). A data warehouse for browsing gene reports, running gene list enrichment analysis, exporting data tables, and saving or sharing work.

	* JBrowse (https://apps.araport.org/jbrowse/?data=arabidopsis). A genome browser hosting about 100 data tracks including 1001 genomes data. Users can also upload and view their own data for side-by-side comparison.

	* Science Apps (https://www.araport.org/apps/catalog). A growing collection of data or analysis modules that will serve as building blocks for creating discovery workflows.

	* Araport11 (https://www.araport.org/data/araport11). Comprehensive updates to Col-0 genome annotation completed and submitted to NCBI for final review.  

	* Tutorials (https://www.araport.org/tutorials). Video tutorials for assessing ThaleMine and JBrowse data.

For questions and comments, please contact araport from jcvi.org.  

Happy Holidays from the Araport team!

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Araport is funded by the US National Science Foundation and the UK Biotechnology and Biological Sciences Research Council.  Araport is a collaborative project started in 2013. Participating groups include J. Craig Venter Institute, Texas Advanced Computing Center, and the University of Cambridge.



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