Release Notes

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SeqLighter v1.0 Release

A sequence widget is now available within our JBrowse to allow users to view and enhance the nucleotide sequence of a selected gene model. Users can highlight regions such as exons, introns, UTRs and start/stop codons, add flanking regions up to 4kb as well as download an image file of the decorated sequence in png, jpeg and svg format. Click here to view a brief tutorial.

ThaleMine 1.1 Release

ThaleMine was upgraded to v1.1.0-8727ce8 [2014-09-26 16:30:00]. The ThaleMine app is available at https://www.araport.org/

Release Notes

Major Changes

  • Enabled downloads of FASTA for gene flanking regions [MINE-288]
  • Fixed problem of FASTA buttons not providing intron sequence [MINE-317]
  • Added JBrowse widget to Exon and Intron pages [MINE-303]
  • Removed limit on Query results (was 10,000 rows) [MINE-329]
  • Added section of External Links on every Gene page [MINE-319 ]
  • Date specified for data provided by TAIR [MINE-265]
  • Improved search results for search terms that include wildcards [MINE-322]
  • Enabled search to find GO terms with hyphen even if user omits the hyphen [MINE-318]
  • Enabled search for terms like "protein complex" to find genes (was finding mRNA only) [MINE-316]
  • Improved summary text layout on Gene, mRNA, and Protein pages [MINE-341]
  • Provided full descriptions instead of bare IDs (e.g. interpro domain IDs) [MINE-323]
  • Removed or enhanced many "Dead End" pages (i.e. pages with little information and no links) [MINE-271]

Minor Changes

  • Upgraded to latest version of InterMine source code [MINE-201]
  • Upgraded to more reliable software for the database connection pool [MINE-146]

Known Issues Not Yet Resolved

  • Detail pages load slowly in recent versions of FireFox [MINE-313]
  • Fix selection of table rows when viewed from some mobile phones [MINE-312]
  • Display co-regulation data [MINE-68]
  • Allow user to export interactions data shown in the Cytoscape/Flash graph viewer [MINE-175]
  • No author displayed for publications written by a consortium [MINE-300]

ThaleMine 1.0.0 Release

ThaleMine was upgraded to version 1.0.0. The ThaleMine app is an instance of InterMine software that is specific to Arabidopsis thaliana and runs on the Arabidopsis Information Portal (www.araport.org). ThaleMine was upgraded to v1.0.0-5ce24ec on 2014-07-18 and to v1.0.0-6bcda48 on 2014-07-21.

Release Notes

Major changes:

  • This is the first version of ThaleMine that uses site-wide login. Now, users only need one username+password registration for all parts of the Arabidopsis Information Portal. (Previously, AIP users needed a separate registration for ThaleMine. Users who had registered during "Preview" releases will need to re-register.) The new login is based on industry-standard technology called OAuth2. It enables single-sign-on across all cooperating web sites, including many popular commercial internet sites. Although registration at AIP is not required for using ThaleMine, registration offers benefits including being able to save and share lists.
  • This version of ThaleMine offers a new widget called "Publications Enrichment". The new widget appears on pages with saved lists, along with older widgets like Gene Ontology Enrichment. Both of these widgets find objects (publications or GO terms) that are statistically overrepresented on ThaleMine pages for the genes in your list.
  • A previous release had reduced the number of "Friendly Mines" displayed on gene pages. Friendly Mines are instances of InterMine at other web sites. ThaleMine's gene pages displays links to orthologs at these other Mines. The temporary reduction was a work-around for a slow-page-refresh issue. The issue is resolved and the Friendly Mines list is fully restored in this release.

Minor changes:

  • ThaleMine 1.0.0 is built with InterMine 1.3.8 software.
  • This version of ThaleMine does a better job of displaying provenance information i.e. the Name, Description, URL and version associated with each data set.
  • This version of ThaleMine fixes a data problem that had caused certain queries to fail. Previously, queries for all interactors with a given gene could fail. This was fixed by assigning a default publication (default = Geisler-Lee, J. et al., 2007) and default interaction type (default = MI:1110, predicted interaction) to all imported data rows these data elements.
  • The summary section (top stripe) of all report pages has a better layout that aligns field tags with their values.
  • This version of ThaleMine gives users the option to fill out a form or send email when the app displays an error. Previous versions had offered a "mailto" link that automatically opened an email client, a feature that some users found annoying. Please continue to send us feedback!
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