[Arabidopsis] Araport Newsletter Summer 2016

Krishnakumar, Vivek via arab-gen%40net.bio.net (by vkrishna from jcvi.org)
Tue Jun 28 18:17:32 EST 2016


Greetings Arabidopsis researchers!


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**What's new in Araport**


(1) We are pleased to announce the official release of the latest
Arabidopsis genome reannotation effort “Araport11” (dated June 20, 2016).
The Araport11 dataset is now available via ThaleMine, JBrowse, Downloads,
and Science Apps.  A draft manuscript describing the Araport11 annotation
can be found at http://dx.doi.org/10.1101/047308.


Quick links:


* Araport Downloads, https://www.araport.org/downloads

* ThaleMine, https://apps.araport.org/thalemine/

* JBrowse, https://apps.araport.org/jbrowse/?data=arabidopsis

* Science Apps, https://www.araport.org/apps/catalog


NCBI GenBank has also accepted and made the Araport11 annotation public,
accessible via the following URLs:


* NCBI (chromosome 1), http://www.ncbi.nlm.nih.gov/nuccore/CP002684

* NCBI (chromosome 2), http://www.ncbi.nlm.nih.gov/nuccore/CP002685

* NCBI (chromosome 3), http://www.ncbi.nlm.nih.gov/nuccore/CP002686

* NCBI (chromosome 4), http://www.ncbi.nlm.nih.gov/nuccore/CP002687

* NCBI (chromosome 5), http://www.ncbi.nlm.nih.gov/nuccore/CP002688


(2) We have added a new RNA-seq expression displayer to the ThaleMine Gene
Report page, and RNA-seq read alignment tracks to JBrowse. The RNA-seq data
collection contains 113 public datasets from 11 tissues.


Example quick links:


* ThaleMine Gene Report (ABI3/AT3G24650):
http://www.araport.org/locus/AT3G24650

* JBrowse RNA-seq (ABI3/AT3G24650):
http://www.araport.org/locus/AT3G24650/browse?tracks=Araport11_gene_models,dark_tophat,dark_tophat_bam



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**Araport at ICAR 2016** (http://icar2016.arabidopsisresearch.org/icar2016/)


Come see Araport at ICAR 2016, South Korea (Talk, Araport Forum & Poster)


* Talk at Session 20 (Room 300C), Saturday July 2, 11.00am - 12.30pm (Chris
Town)

* Araport Forum (Room 101, 102), Saturday July 2, 07.00pm - 08.30 pm
(Araport, IAIC and community contributors)

* Poster (P535) in the New Technology session


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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  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 close to 100 data tracks including population variant data
from the 1001 Genomes Project. 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 including gene structures and functional
annotation.


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


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



******

The Araport team

******


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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