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Genome Data Viewer (GDV)

What's New

Genome Data Viewer, version 5.1, May 2021

  • New Features and Improvements
    • Sequence Viewer updated to version 3.42
    • JIG version updated to 1.15.3
    • Updated to Generic Browser Components 2.7.16
    • Improved navigation using the web browser back button
    • A selection of annotated GenBank assemblies can now be viewed in GDV
    • Renamed Add Tracks widget to Add Tracks by Accession
    • Additional minor updates and bug fixes

Previous Releases

Genome Data Viewer, version 5.0 Released March 1, 2021

  • New Features and Improvements
    • Updated to Generic Browser Components 2.7.15
    • GDV is now released on the NCBI Django platform
    • Track collections can be specified in the GDV URL parameters for easier sharing of GDV views

Genome Data Viewer, version 4.8.12 Released Jan 21, 2021

  • New Features and Improvements

    • Updated to Generic Browser Components 2.7.12
    • Added an inline help box on the home page
    • Web browser back button will now take you to the previous view of the GDV home page
    • Updated default assembly settings for some organisms (e.g. rat, dog)
  • Bug Fixes

    • Corrected reporting of scaffold numbers in the Ideogram panel for the GRCm39 assembly (GCF_000001635.27)
    • Fixed a bug in adding markers when the marker is specified in the URL
    • Fixed a bug in the behavior of the BLAST widget
    • Updates to labels on the GDV home page

Genome Data Viewer, version 4.8.11 Released Nov 17, 2020

  • New Features and Improvements

    • Updated to Generic Browser Components 2.7.11
    • New table view option on the home page for navigating and selecting organisms and assemblies
    • Ended GDV user survey
  • Bug Fixes

    • Fixed broken links when accessing GDV from the dbGaP search page

Genome Data Viewer, version 4.8.10 Released July 29, 2020

  • New Features and Improvements

    • Updated to Generic Browser Components 2.7.10
    • New ability to download the sequence of exons in a transcript variant from the Exon Navigator panel
    • Searches for non-chromosome scaffolds now finds and displays the corresponding location on the chromosome assembly (if available) with the scaffolds track opened in the graphical viewer
    • Added a link to a user survey
  • Bug Fixes

    • minor bug fixes

Genome Data Viewer, version 4.8.9 Released June 22, 2020

  • New Features and Improvements

    • Updated to Generic Browser Components 2.7.9
    • Information panels for search results from the GDV browser and home page now report expanded information, including the full gene, transcript, or protein name, and the gene summary and other names if available
    • A URL containing an assembly accession without a specified version (e.g. ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_000001405) will now open the latest assembly version by default
  • Bug Fixes

    • Search results will now only show results on the latest equivalent assembly version and not show redundant results

Genome Data Viewer, version 4.8.8 Released May 20, 2020

  • New Features and Improvements

    • Updated to Generic Browser Components 2.7.8
    • Now showing top 30 scaffolds for scaffold-level assemblies in the Chromosome selector menu
    • The "More..." option in the Chromosome selector menu links to an NCBI Nucleotide database page listing all scaffolds in an assembly
  • Bug Fixes

    • Brought back support for searching by NCBI dbVar identifier (e.g. nsv532230)
    • Fixed minor bugs that resulted in error pop-ups when going to an assembly or pressing the back button on the browser
    • Fixed links to chromosomes from the GDV landing page ideogram
    • Additional minor bug fixes

Genome Data Viewer, version 4.8.7 Released April 21, 2020

  • New Features and Improvements
    • Updated to Generic Browser Components 2.7.7
    • New ability to hide the left sidebar using the << button or pressing the "[" key
    • New search box appears on the top left of the page when left sidebar is hidden
    • New dropdown menus on the top of the page to select assembly and chromosome
    • Additional design and color changes to the page header
    • Improvements to user experience using touchscreen mobile devices
    • GDV search now supports coordinates using 'c' for complementary strand; e.g. NC_000017.11:c43125364-43044295
    • Updated Help Documentation
  • Bug Fixes
    • Fixed a bug in searching after switching assemblies
    • Fixed a bug in expanding the input box to add remote URLs or text data in the User Data widget
    • Fixed a bug in remembering the user settings after visting the GDV landing page
    • Announcement banner no longer appears in the same session after it has been hidden by clicking x

Genome Data Viewer, version 4.8.6 Released March 11, 2020

  • New Features and Improvements
    • N/A
  • Bug Fixes
    • Security patch
    • Restored back button to graphical viewer

Genome Data Viewer, version 4.8.5 Released March 5, 2020

  • New Features and Improvements
    • Updated to Generic Browser Components 2.7.6
    • Assembly information and search box now located on the upper left of the page
    • Go directly to search or BLAST results using markers on the chromosome region selector or ideogram
    • Additional design changes to the header of the page including consolidation of information within links and an updated NCBI/NLM info bar
  • Bug Fixes
    • Minor bug fixes in gene searches from the search box

Genome Data Viewer, version 4.8.4 Released January 9, 2020

  • New Features and Improvements
    • Updated to Generic Browser Components 2.7.5
    • Improved navigation within the region selector ideogram allows users to click and drag to zoom to a custom region and click to zoom directly to a chromosome band
    • A marker is now created at the corresponding region in the graphical viewer upon searching within the browser or GDV landing page for a single nucleotide coordinate or SNP
  • Bug Fixes
    • Minor bug fixes

Genome Data Viewer, version 4.8.3 Released November 14, 2019

  • New Features and Improvements
    • Updated to Generic Browser Components 2.7.4
    • URL is updated when assembly is changed using the Pick Assembly widget
    • Improved error messages when adding remote tracks that are a mapped to a different genome assembly
  • Bug Fixes
    • Fixed bugs that affected the order of tracks added in the graphical sequence viewer
    • Fixed a bug which allowed remote tracks to be added to an incompatible assembly
    • Fixed a bug causing inconsistencies in track display settings set in the Configure Track hubs menu and the graphical view configure menu

Genome Data Viewer, version 4.8.2 Released October 11, 2019

  • New Features and Improvements
    • Updated to Generic Browser Components 2.7.3
    • New options in Configure Track Hubs menu allow user to add or remove default hub tracks in bulk
    • Updated Configure Track Hubs menu help documentation
    • Added a Pick Assembly widget that allows users to switch to compatible assemblies for the same species
    • Improved performance of loading of BLAST results
  • Bug Fixes
    • Fixed a bug in remembering the track order when the page is reloaded or shared
    • Fixed a bug in displaying BLAST results when arriving from the NCBI BLAST resource page
    • Remote and BLAST tracks will no longer shown by default when the browser view is reset

Genome Data Viewer, version 4.8.1 Released September 9, 2019

  • New Features and Improvements
    • Updated to Generic Browser Components v.2.7.2
    • Default hub tracks are now shown in the graphical display when track hubs are connected via the Track Hub Registry
    • Added exon numbering to the exon navigator
    • UI improvements to User Data and Track Hubs, Configure Track Hubs dialog, and exon navigator
    • Added help documentation for User Data and Track Hubs and the Configure Track Hubs dialog
  • Bug Fixes
    • Fixed several bugs in the BLAST Inspector and BLAST widget
    • Fixed a bug in sorting of newly added tracks in the graphical display
    • Fixed an error in rendering data from some alignment tracks
    • Fixed a bug in loading the GDV homepage in Internet Explorer version 11

Genome Data Viewer, version 4.8. Released July 25, 2019

  • New Features
    • Tabix VCF files can be added as remote files (URL) or via track hubs
    • Exposed additional information including the remote track URL in the User Data and Track Hubs widget and Configure Track Hubs interface
    • UI updates to the User Data and Track Hubs widget
    • Added the ability to drag and drop multiple URLs into the User Data and Track Hubs widget
    • Updated to Generic Browser Components v.2.7.0
  • Bug Fixes
    • Fixed a bug in the ordering of tracks originating from dbGaP relative to default tracks in the genome browser
    • Fixed a bug preventing sharing of user uploaded tracks when using the "Share this page" option
    • Fixed a bug in retaining track display settings when using the 'Share this page" option or reloading the page
    • Fixed a bug in searching the Track Hubs Registry from the Configure Track Hubs interface
    • Fixed a bug in searching for Genes using the Search widget

Genome Data Viewer, version 4.7. Released February, 2019

  • New Features
    • Implemented comment card to capture user feedback
    • Added support for track hierarchies specified in hubs; see Help documentation for usage details
    • Updated to Generic Browser Components v.2.6.3
  • Bug Fixes
    • Fixed bug that resulted in tracks from hubs added in GDV appearing by default in graphical displays in other NCBI resources (e.g. NCBI)

Genome Data Viewer, version 4.6. Released October, 2018

  • New Features
  • Bug Fixes
    • Fixed bug that resulted in use of wrong browser context in URL when using "Share this Page option

Genome Data Viewer, version 4.5. Released July, 2018

  • New Features
    • "Your Data" widget redesigned as "User Data and Track Hubs" to include Track Hubs related options
    • Added new functionality and user interfaces to support connection to and configuration of tracks organized as Track Hubs; see Help documentation for usage details
    • Use of the Track Hub Registry for hub search
    • Updated to Generic Browser Components v.2.6
    • Added Feedback button option to collect user input

Genome Data Viewer, version 4.4. Released February, 2018

  • New Features
    • Added ability to remotely stream and display BAM tracks as custom data type; see Help documentation for usage details
    • Updated to Generic Browser Components v.2.5
    • Improved warning and error text associated with custom data tracks in Your Data widget
  • Bug Fixes
    • Fixed bug that could lead some BLAST query titles appearing as "undefined" in the BLAST widget and BLAST Alignment Inspector
    • Fixed bug interfering with searches using top-level assembly accessions on the GDV home page
    • Fixed bug causing loss of some track display settings when web browser tabs were closed or pages reloaded

Genome Data Viewer, version 4.3. Released October 24, 2017

  • New Features
    • BLAST widget added to GDV; see Help documentation for usage details
    • Updated to Generic Browser Components v.2.4
  • Bug Fixes
    • Fixed bug affecting tooltips in Assembly Region Details widget
    • Improved panel closure via use of Esc key so that it is limited only to the most recently opened panel

Genome Data Viewer, version 4.2. Released April 26, 2017

  • New Features
    • Ideogram View widget updated to provide count of unlocalized/unplaced and alternate loci/patch scaffolds
    • Exon Navigator widget added to GDV; see Help documentation for usage details.
    • Added support for drag-and-drop repositioning of left-side page widgets (e.g. Ideogram View, Search, Your Data, etc)
    • Added GDV representations for contig- and scaffold-level assemblies
    • Added GDV representations for organisms annotated via the NCBI small eukaryotes pipeline
    • Updated GDV header to show exact assembly coordinates when there is sufficient browser width
    • Added support for keyboard navigation of GDV pull-down menus
    • Improved functionality of URL parameters ('q' and 'acc'; see Help documentation for more information)
    • Web browser history now recognizes changes in genome location and records gene/transcript/exon selections
    • Updates to support use of new back-end services supplying data to Exon Navigator and Assembly Region Details widgets
    • Updated to Generic Browser Components v.2.3
  • Bug Fixes
    • Fixed bug affecting display layout in MS Edge
    • Prior track selections no longer lost when switching back and forth between assembly versions
    • Fixed bugs associated with display and location when using 'Share this page' option

Genome Data Viewer, version 4.1. Released August 29, 2016

  • New Features
    • Back end update to support improved logging
  • Bug Fixes
    • Fixed bug affecting display of Gene history when reloading the page

Genome Data Viewer, version 4.0. Released July 5, 2016

  • New Features
    • Navigation for URL-specified features (genes, transcripts and proteins). The "Pick Assembly" widget now contains a table providing all locations for features specified in the "acc" parameter of the GDV URL in the selected assembly. Clicking on a table row updates GDV to the corresponding location.
    • Highlighting for URL-specified features (gene, transcripts and proteins). The feature specified in the "acc" parameter of the GDV assembly is now highlighted with a gray box in all tracks in which it is displayed in the graphical view.
    • Added "Region Details" widget to GDV. This widget provides information about other features of interest relevant to the displayed region, including any alternate loci or patch scaffolds. For genomes assemblies curated by the Genome Reference Consortium, it includes a link to add the GRC issues track that highlights assembly regions under review (human, mouse, zebrafish, chicken).
    • Back-end updates to support specification of gene, transcript and protein features in GDV URL.
  • Bug Fixes
    • Added support for searches for unlocalized and unplaced scaffolds.

Genome Data Viewer, version 3.0. Released January 8, 2016

  • New Features
    • Back-end updates to support use of assembly accession as a parameter in browser URL
  • Known Issues
    • Search functionality in GDV may be limited for assemblies that are not in the NCBI Map Viewer . This issue affects searches for transcripts, proteins and phenotypes, but not searches for locations, genes or SNPs.
    • Searches for unlocalized or unplaced scaffolds return no results.

Genome Data Viewer, version 2.0. Released November 2015

  • New Features
    • Added Track Sets and Track Collections
    • Added "Add Tracks" widget, which supports 1-click addition of GEO or SRA tracks to the display by accession.
    • Searches like "4:10000000" or "X:3000000-35000000" are now treated as location searches, equivalent to "chr4:10000000" or "chrX:30000000-35000000". The "chr" prefix for chromosome names can be omitted in location searches.
    • Search now supports GenBank sequence identifiers like CM000667.2 and HSCHR6_MHC_APD_CTG1. These can also be combined with more specific genomic coordinates, e.g. CM000667.2:1000000-1500000.
    • The first search result is now automatically selected if its name matches the searched term. For example, searching "APOE" or "rs334" seamlessly loads APOE or rs334 into view, without users needing to manually select the first row.
    • Improved usability in the Your Data widget; users can now specify track names for uploaded data
  • Bug Fixes
    • When using the "Share this page" link, the selected assembly is now properly maintained.

Genome Data Viewer, version 1.0. Released August 2014

  • Features
    • Initial release of the Genome Data Viewer
    • Accessed through GEO
    • Pick Assembly
    • ID Search
    • User data upload
    • Custom linking with URL parameters
  • Known Issues
    • Compromised performance when large numbers of tracks (>200) are loaded to the display
    • "q" parameter in URL does not work for non-nuclear genes. Note: Non-nuclear genes can be searched via the "Search" widget, but the "q" parameter will not return data for non-nuclear genes. This will be addressed in a future release.
    • When using IE11, user-uploaded tracks may fail to appear in the "Your Data" widget if uploaded after deleting tracks from this widget. Refreshing the browser, or re-loading the track will resolve the issue. This issue is not seen in Firefox or Chrome, and will be resolved in the next GDV release.