Release Notes

×

Status message

New Feature: Guest Login function added to facilitate site exploration without registering. Try it out!

ThaleMine 1.6.2 Release

ThaleMine was updated to version 1.6.2 on 27 August 2015. ThaleMine is available at https://apps.araport.org/thalemine/

Release Notes

Minor Changes

  • On ThaleMine list sharing invitation emails, clicking on the invite URL now correctly triggers the appropriate workflow [FEED-462, FEED-504, MINE-968]
  • On ThaleMine My Mine page, usernames can now be specified without the ARAPORT: prefix when sharing lists [FEED-504, MINE-338]

ThaleMine 1.6.1 Release

ThaleMine was updated to version 1.6.1 on 26 June 2015. ThaleMine is available at https://apps.araport.org/thalemine/

JBrowse was updated on 26 June 2015. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis

Release Notes

Major Changes

  • ThaleMine 1.6.1 runs InterMine 1.5.3, the latest version of the software [MINE-850]
  • ThaleMine 1.6.1 incorporates a Pathway Enrichment widget on List Analysis pages [MINE-838]
  • ThaleMine 1.6.1 excludes the non-curated Reactome pathway dataset [MINE-821]

Minor Changes

  • On ThaleMine gene report pages, the embedded JBrowse has been cleaned up to hide all controls, making it appear as an image representation of the gene structures [MINE-399]
  • On ThaleMine protein report pages, the Protein Domain displayer now correctly organizes the features alongside a reference coordinate system and adds appropriate feature labels [MINE-309]
  • On ThaleMine dynamic result tables, unexpected expansion of the table cells on mouse-over has now been fixed [MINE-832]
  • On ThaleMine dynamic result tables, the web service URL in the generated code now correctly uses the https prefix [MINE-853]
  • In JBrowse, the display of genotype/phenotype information in the 1001 Genomes Variants track is now triggered using a left-click instead of via the right-click context menu [MINE-870]
  • In JBrowse, the filtering of 1001 Genomes Variants track data now offers a bulk toggle option per major variant type [MINE-858]

ThaleMine 1.6 release

ThaleMine was updated to version 1.6 on 26 May 2015. ThaleMine is available at https://apps.araport.org/thalemine/

JBrowse was updated on 26 May 2015. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis

Release Notes

Major Changes
  • ThaleMine 1.6 incorporates a Protein Domain Displayer on protein report pages [MINE-309]
  • ThaleMine 1.6 incorporates the following updated datasets:
    • TAIR curated data through 03/31/2014 (second public release). Compared to ThaleMine 1.5.1, this version has 37 new or updated gene symbols and 25 new or updated curator summary fields [MINE-782]
    • Gene-to-publication mapping from NCBI gene2pubmed, updated to release 04/20/2015 [MINE-780]
    • Curated Gene Reference Into Function (GeneRIF) annotation of gene records from the NCBI gene database, updated to release 04/20/2015 [MINE-781]
    • GO annotations from geneontology.org, update to release 03/31/2015 [MINE-782]
    • Protein domain data from InterPro, updated to release v51.0. Protein domains now include coordinates (signatures) from InterPro protein2ipr [MINE-789]
    • Curated (SwissProt) and Computationally derived (trEMBL) protein data from Uniprot, updated to release 2015_05 [MINE-790]
    • Homology data from Panther, updated to release v10.0 [MINE-791]
  • JBrowse incorporates the following new community datasets:
    • Annotations for 166,439 insertions identified in 100,013 existing segregating T-DNA insertion lines (from SALK, SAIL, WISC, and GABI-kat collections) identified using TDNA-seq technology developed in the Ecker laboratory (O'Malley et al, unpublished) [MINE-750]
    • 40,131 RBP-binding sites detected using protein interaction profile sequencing (PIP-seq) on total nuclei from 10-day-old seedlings from the Gregory lab (Gosai et al, 2015) [MINE-777]
Minor Changes
  • On ThaleMine gene report pages, every data stripe now has a “Data Source” tag, with a link out to a page describing the data source and version number [MINE-769]
  • On ThaleMine gene list pages or template query pages, selecting “Log in to save your list/template permanently”, now correctly directs the user through the login process and subsequently stores their data [MINE-783]
  • In JBrowse, the glyphs used to represent polymorphism features have been updated [MINE-490]
  • In JBrowse, the user help guide has been refactored and updated to better describe Araport specific plugins and features. Updated user guide is available at https://www.araport.org/jbrowse/user-guide [MINE-808]
Subscribe to Release Notes