Release Notes

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Portal - May 2015

The Araport Portal was updated on May 4, 2015. This update includes a new homepage, menu and page organization, as well as several new features. The new menu and page organization reflects the focal points of the Araport Portal and is designed to guide users more quickly to the features and information they are seeking.

New Features

  • API Explorer - The API Explorer allows users to explore the Community Data, Agave, and Thalemine APIs that power the Araport Platform
  • Apps Catalog - The Apps Catalog shows a view of all public apps available on the Araport Portal.
  • iPlant DataStore Integration - Araport Users can now easily configure their iPlant DataStore for access through Araport. From your user page select the iPlant DataStore tab. Users can activate your iPlant DataStore for Araport by providing their iPlant Username and Password. Once configured, the iPlant DataStore is available as a Storage system in the Araport Agave API. It is also browsable using the new File Browser app.
  • Araport Service Monitor - Monitoring of the current status of Araport Platform services (displayed on the homepage).
  • Araport RFC - Community Requests for Comment.

New Apps

  • File Browser The Araport File Browser is a new app that allows users to browse all the Storage systems they have configured in Araport Agave API Tenant.

ThaleMine 1.5.1 Release

ThaleMine was updated to version 1.5.1 on 17 April 2015. ThaleMine is available at https://apps.araport.org/thalemine/.

Release Notes

Minor Changes

  • JSON Web Tokens (JWT) used for authenticating ThaleMine web service calls are now parsed to retrieve the correct enduser claim [MINE-764]
  • Web service documentation for ThaleMine now presents Arabidopsis specific example queries [MINE-776]

ThaleMine 1.5 Release

ThaleMine was updated to version 1.5 on 03 April 2015. ThaleMine is available at https://apps.araport.org/thalemine/.

JBrowse was updated to version 1.11.6 on 03 April 2015. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis.

Release Notes

Major Changes

  • ThaleMine 1.5 incorporates homologs of Arabidopsis genes in many plant species computed by JGI using the InParanoid protocol and acquired from the Phytozome database [MINE-173].
  • ThaleMine 1.5 incorporates mappings between Arabidopsis transcripts and their corresponding curated protein records from UniProt [MINE-445].
  • JBrowse 1.11.6 incorporates a variant track from the 1001 Genomes project. Variant features are color coded using Ensembl's consequence diagram, and track data can be filtered by variant type [deletion, insertion, snv, etc.] and by consequence type [missense, intron_variant, frameshift variants, etc.]. Variation Features popup (available via a right-click menu) retrieves genotype, population and phenotype data using Ensembl's REST service. [MINE-709]

Minor Changes

  • On ThaleMine gene or protein detail pages, in the Publications stripe, the source of the publication is now displayed as NCBI or UniProt, respectively [MINE-485].
  • On ThaleMine gene or protein detail pages, in the Publications stripe, the records are now sorted in reverse chronological order [MINE-726].
  • On a ThaleMine gene detail page, clicking on a GeneRIF now directs to a publication detail page with information about genes/proteins referenced in the publication [MINE-714].
  • On a ThaleMine protein detail page, keywords from UniProt are now displayed in the summary at the top of the page [MINE-294].
  • On ThaleMine detail pages, the external links on the right hand side are now ordered alphabetically and display a popup, on mouseover, with a brief description about the external database [MINE-443].
  • On any ThaleMine page, clicking on the “Contact Us” link at the top (right) or the bottom (left) of the page now correctly focuses the user to a pre-filled contact form with details about errors, if any, encountered on the current page [MINE-454].
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