EnsemblEnsembl Home

Ensembl Web News

Release 88

Masthead redesign (all species)

As we begin to incorporate strains and other non-reference assemblies into Ensembl, we want to display more information about a "species" on all relevant pages so that users are aware of the differences.

We have therefore rearranged the top of our browser pages, removing the species "tab" and putting the information in the dark blue area above the tabs where there is more space. The dropdown list of species is still accessible via the triangle icon, and all other functionality is unaffected.

Find a Data Display (all species)

Ensembl has lots of different pages where you can access data or see visualisations of that data. Now, to help you find the display you need, we have introduced our "Find a data display" page. Just type a gene identifier, location or RSID into the form to see a list of relevant views, with thumbnails of sample data and links to that page for your feature or region of choice.

The page can be accessed from the central panel on the home page or via the 'Help and Documentation' link in the page header - in the latter, the link is near the top of the lefthand menu.

Release 87

New table on Regulation Summary page (all species)

Now that we have many dozens of epigenomes in the Regulatory Build, we can no longer show them all on the Regulation Summary image by default. We have therefore added a table listing the cell types by their regulatory feature activity.

Minor changes to ontology tables (all species)

In order to clarify the source of gene ontology information, we have separated the data previously displayed under 'Annotation source' into 'Annotation source' and 'Mapped using'. The latter column is hidden by default but can be displayed by clicking on the 'Show/hide columns' button in the table header.

Sorting of RNAseq matrix (Zebrafish)

We are in the process of adding a sort order to the rows in the RNAseq matrix in the Region in Detail configuration menu. Initially this will be applied to zebrafish only, to sort the developmental stages into a logical order, but it may be rolled out to other species in due course as appropriate.

Release 86

Session code rewrite (all species)

The way the ensembl webcode interacts with session and accounts databases and saves user configurations has been changed. The code interacting with mysql database has been removed and the webcode now uses ensembl-orm API to access session database.

Parts of ensembl-webcode where major changes are expected are Apache Handlers, Controllers, ImageConfig and ViewConfig.

Further description can be found on GitHub

BigWig Manhattan plots (all species)

In this release, we've added the ability to display your bigWig data as a Manhattan plot:

Simply select 'Manhattan plot' from the track style list after loading.

Orthologue Table redesign (all species)

The orthologue table has been redesigned slightly with the aim of inproving usability. It also accomodates three new metrics representing the confidence of our ortholgue predictions - Gene Order Conservation (GOC) Score, Whole Genome Alignment (WGA) Coverage, and High Confidence.

Variation track style consolidation (all species)

The code for drawing our SNP and indel variation tracks has been consolidated so that tracks will appear the same across all views.

Summary of changes

  • Deletions are drawn as a block spanning the deleted area, with the addition of a downwards-pointing triangle symbol superimposed.
  • Insertions are drawn the same way as before, but are enlarged at smaller scales for better visibility
  • Variation tracks on Protein Summary are drawn the same way as on other images, instead of as tiny squares and triangles, and can thus be configured as different styles, eg. with labels

In addition to the visual changes, we have also fixed some bugs with variant placement on Protein Summary.

New views added for mobile site (all species)

You can now view details of Transcripts on the mobile site, for example the Summary page, and sequence of Exons, cDNAs and proteins. We also added the gene sequence display to the site.

To view the sequence pages, please click on the left hand arrow icon which will open a menu allowing you to choose the relevant view you want.

Mobile site redirection (all species)

Users on mobile phones will be automoatically redirected to the mobile version of the site when you visit www.ensembl.org for the first time. You can choose to view the desktop site by clicking on the link at the bottom of the screen.

New comparative genomic views for strains (all species)

The mouse strains resources (mouse reference assembly, mouse strains and rat reference assembly) have a separate left hand menu for their own comparative genomics resources which includes gene trees, orthologues and paralogues.

New species selector (all species)

New species selector user interface designed for Blast, Region Comparison and Alignment Selector with below features.

  • Search
  • Division based species selection
  • Add/remove/sort species

Mouse strain search (Mouse)

The addition of mouse strain data is accompanied by changes to the search interface to allow this data to be found but without overwhelming the results in other circumstances.

By deafult, only reference mouse hits are shown. By faceting on mouse, all hits on strains are also shown, along with a further faceting option to refine that selection.

Mouse strain variant table (Mouse)

A new location display, "Strain table", visible for Mouse location displays, shows variants between mouse strains within the region in a tabular form.

GTEx beta value display (Human)

The GTEx per-tissue variant expression data for genes can now be configured to display beta-distribution values, instead of log-p-value figures. This is configured by altering the track renderers. These tracks have also been moved out of "Other regulatory regions" into their own section, directly under the general Regulation heading.

Retirement of archive 73 (all species)

This release cycle we will be retiring archive 73 (September 2013) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Release 85

Removal of old online tools (all species)

The following information is principally for the developers of Ensembl-powered websites:

In release 85 we are removing the old versions of our online tools - the ones that can be found under 'Personal Data' in previous releases, i.e. the original versions of the VEP, assembly converter and ID history converter. The underlying software is no longer being maintained, and you should switch your site to using the new versions (as seen on the main Ensembl website).

More information about setting up the new Tools infrastructure can be found in our online documentation.

Retirement of archives 71 and 72 (all species)

This release cycle we will be retiring archives 71 (April 2013) and 72 (June 2013) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Userdata & Track highlighting (all species)

We have added or changed the following functionality in Location View

  • Userdata highlighting
    • When you upload your data, the track showing it will be automatically highlighted. The highlight will disappear on hover
  • Highlight track on hover
    • When placing the cursor over a track, the whole width of the track will be highlighted
    • [screenshot]
  • Track menu Highlight Icon
    • An icon is provided in the track menu that allows you to manually turn highlighting on/off
    • [screenshot]
  • Track menu click behaviour
    • To accommodate the track highlighting feature described above, the menus that previously appeared when hovering over a track label now only appear after clicking on it.

Wasabi Tree viewer (all species)

We have replaced Jalview with Wasabi as an additional way of viewing gene trees and multiple alignments. It is accessible by clicking on any node within a gene tree.

A menu with option "View in Wasabi" is provided as below


And it will open up a popup window with the tree and alignment as shown below.


SNPedia descriptions (all species)

We now fetch descriptions for human variants from SNPedia.com (wiki) and where available display the information on the Variant Summary page. An example is below:


File Chameleon (all species)

Want to use Ensembl data for your analysis tool? We now have a new tool to do this for you. File Chameleon will customise files from the Ensembl FTP server.

Please note that File Chameleon doesn't convert between file formats. Current features include:

  • adding 'chr' to your chromosome names for use with UCSC's genome browser
  • remove long genes

Remove account settings from personal tab (all species)

To make the personal data tab in the configuration panel less confusing we have removed account related information from it. The personal tab now only holds information about your uploaded data, attached Track hubs, and saved configurations for tracks.

Account related information is still available from the 'My Account' window. To access this you need to log in to the site and then click on your email address which will appear at the top right of the page.

GTEX eQTL data (Human)

GTEX eQTL data for 14 tissues has been added to the Gene Regulation view for human.

Transcript version display (all species)

You can now see the transcript's version displayed alongside the transcript stable ID on the transcript table and inside the zmenu

Change in title for user data buttons and pages (all species)

To simplify our interface, we have renamed the page where you upload and manage your own data to 'Custom tracks', and merged the 'Add data' and 'Manage data' pages into one. The functionality of these pages has not otherwise changed.

Validating track hubs with hubCheck (all species)

We now validate any track hubs that are not attached via the Track Hub Registry Search, using UCSC's hubCheck utility. If you try to attach a hub and it does not validate, you will need to contact the hub creator; their email address should be listed in the hub.txt file.

Track hubs from the registry are pre-validated with hubCheck, so additional checks are not necessary.

Text Alignment View Show/Hide full alignment (all species)

Text alignment view will show a small block of 120 columns initially with an option to view the full alignment there by reducing page load delays. Turn on/off full alignment view using the button provided. 

Image below shows an example of the initial display.


Select species or regions (all species)

Based on the Comapara view usability testing, we have improved the layout of 'Select species or regions'. All unselected species will now be on the left hand side and selected species on the right hand side hoping that there will be less confusion to the users.

Example below


Segmentation feature legend (all species)

The segmentation feature track now has its own legend, which will appear when you turn on any segmentation track.

Release 84

Track hub registry interface (all species)

With the arrival of the new Track Hub Registry, we have added a page where you can search for track hubs of interest and attach them directly to Ensembl. Just click on the 'Add your data/Manage your data' button on e.g. Region in detail, and select 'Track Hub Registry Search' from the lefthand menu.

The interface will only search for hubs that have assemblies available for the site you are on; to see the full range of species and assemblies, visit the Track Hub Registry site directly.

Pairwise LD calculation on LD variant page (Human)

Starting from a variant page, you can calculate LD between the variant from the variant page and your favourite variant. You can enter your favourite variant into a text box and select the population from which to draw the genotype data from from a dropdown list.

CRAM alignments display (all species)

The file upload and trackhub interface has been updated to show alignments in CRAM format in the same way that BAM files are displayed. Simply paste in a URL and 'CRAM' should automatically be selected from the dropdown menu.

Please note that, as with BAM, you will need a sorted index file in the same directory, otherwise we cannot retrieve data from a given region.

GFF3 support for userdata (all species)

Our backend drawing code for users' custom tracks has been upgraded to use the new EnsEMBL::Draw::Style infrastructure, which has allowed us to improve support for various formats as follows:

  • GFF3 has been added as a supported format
  • GFF2 and GTF are now treated as a single format since they are very similar, and transcript structures are shown where available
  • the default display for GFF2/3, GTF, BED and bigBed is now "structure with labels", i.e. transcript-like
  • Graph values (bigwig, etc) which exceed the maximum value on the graph y-axis are cut off at that value, with a black line at the upper edge to denote truncation
  • various other small improvements to parsing and display of existing formats

Please see our custom track documentation for further details.

Developer note: the new code uses parsers from the ensembl-io repository for file upload and display. If you have any file-related custom code under the EnsEMBL::Web::Text (the old parsers) or EnsEMBL::Draw::GlyphSet namespaces, this will need replacing with code from Bio::EnsEMBL::IO::Parser and/or EnsEMBL::Draw::GlyphSet::flat_file (note no underscore at beginning of module name), ::bam, ::bigbed, ::bigwig, ::pairwise and ::vcf.

Saving your uploaded data (all species)

Beginning with release 84, we will no longer save uploaded data into a core-like database, as this leads to loss of information, as well as being unsuitable for some formats such as long-range interactions. Instead we will move the uploaded file sideways to a more permanent location where it will not be removed by our clean-up scripts. Existing saved data will remain accessible until we remove the old databases in release 85.

Note that because files will be stored locally to the website you are viewing, data uploaded on one website cannot be viewed on other sites after saving. E.g. if you upload a file on useast.ensembl.org and then visit uswest.ensembl.org, the file will not be viewable and must be uploaded again.

N.B. These limitations do not affect data attached remotely (BAM, BigWig, etc) as we only store the URL, not the data itself, so this information can easily be tied to your user account.

Transcript haplotype view (all species)

A new view for exploring observed transcript sequences in resequencing data (1000 genomes).

DAS support ended (all species)

As previously announced on the Ensembl blog, from release 84 onwards the Ensembl browser will no longer support the DAS protocol. If you have been using DAS to view your own annotations in Ensembl then we recommend that you create a Track Hub and attach that to Ensembl. Alternatively if you have been using DAS to retrieve our anotation then we suggest you use our REST (rest.ensembl.org) server instead.

Simplified URLs for attaching tracks (all species)

For a long time it has been possible to attach a file to Ensembl using a URL, but the syntax has been non-intuitive. In this release we've added a simpler format - just append


to any Region in Detail (Location/View) link. Note that this doesn't currently work with other images, but we anticipate that this will cover 99% of use cases - and you can still use the old syntax with any page if needed.

Retirement of archive 70 (all species)

This release cycle we will be retiring archive 70 (January 2013) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Mirror redirect behaviour changed (all species)

The way the Ensembl websites redirect users to a nearest mirros has been changed. The website users gets redirectly immidiately to a nearest mirror and then sees a message on the screen informing about the redirect instead of seeing a message first and then getting redirectly to a nearest mirror after 9 seconds.

Location search with commas,_,: and .. (all species)

You can now search for a location with commas, _  and .. and it will send you directly to the location view.

Example of valid location search:

13: 32,315,474-32,315,500

chr13: 32,315,474-32,315,500




Exon numbering (all species)

You can now see the exon number that you have clicked on for a transcript. The exon number will appeared in the popup menu once you clicked on an exon.

Release 83

Filtering Variants by MAF (all species)

The variants displayed on all sequence markup views can be filtered by minor allele frequency (MAF), allowing you to either show or hide according to a range of frequencies (between 0.01% and 10%). This filtering is not on by default so to enable it go to 'Configure this page' and then chose the value you want from the 'Hide variants by frequency (MAF)' drop down menu.

Advanced Filtering and Counts on Variant table (all species)

The functionality of the recently reimplemented variant table has been further expanded to allow a wider range of filtering options. Filtering can now be applied by Minor Allele Frequency, SIFT and PolyPhen scores, Clinical Significance, Consequence Type and many other columns, using buttons along the top of the variant table.

For many of these filters, preset useful combinations of options are available within the popup allowing rapid configuration of more complex combinations.

In addition, row counts for each consequence type have been readded to the existing Consequence Type filter. These are displayed in the popup which appears once the filter button has been pressed.

Improved image export (all species)

As part of our ongoing upgrade of the website export functions, we have a new Image Export "wizard" in place of the old popup menu. This can still be found via the 'picture' icon in the blue bar above images, but it now opens a window with a form where you can choose from a selection of preset options or configure a custom output.


Note that we have removed GFF export from this menu, in preparation for an upcoming revamp of the more general feature-and-sequence export. You can still export genes and a few other tracks from most images by clicking the 'Export data' button in the lefthand menu.

Manhattan plot track for LD (all species)

This new linkage disequilibrium (LD) track is focused on a variant and displays the linked variants surrounding the focus variant. The track displays a Manhattan plot, using the r2 and D prime values (from 0 to 1) on the Y axis.

The new track is accessible from the Variation Linkage disequilibrium page, through the links in the new column "LD Manhattan plot", for example:


Retirement of archive 69 (all species)

This release cycle we will be retiring archive 69 (October 2012) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Ontology view moved (all species)

The Ontology view has been moved from the transcript to the gene panel, with table for the different Ontologies (Biological Process, Molecular Function etc) being shown in seperate views. The tables have an additionall column showing the stabel IDs of the transcruipt(s) to which the term has been mapped. An example is:


Mobile site updates (all species)

The following updates to the mobile site have been released:

  • Improved behaviour when being redirected from www.ensembl.org to m.ensembl.org, for example informative messaging if the requested view is not available
  • Higher resolution share icon
  • Bug fixes (i) added ability to close "Switch to mobile site" banner (ii) logging in no longer redirects you to the desktop site

Vector image export for pairwise interaction data (all species)

Drawing of arcs has now been implemented in our PDF and SVG drawing code, which means that this data can now be displayed in all export formats.

ID History converter (all species)

The ID History Converter has been incorporated into the Ensembl Tools infrastructure. This allows you to save jobs and access them later in a similar manner to how you would for tools such as BLAST.

Genoverse version updated (all species)

The version of Genoverse used for the overview panel on Location View has been updated to version 2.3.

Release 82

Ensembl mobile site (all species)

we now have a mobile version of ensembl at http://m.ensembl.org

You can quickly search for a gene, variants or phenotypes on the mobile site. Have a look and let us know your comments/feedback.

VEP plugins (all species)

Support for VEP plugins through the VEP web interface

Improved data upload form (all species)

The design of the "Add your data" form has revised to make it easier to use. There are now only two input boxes, one for selecting a file on your computer and the other to paste data or a file URL. The form will attempt to identify the file format from the extension (if any), so you will only need to select the format manually if pasting data or if the file extension is ambiguous.

At the same time we are implementing more validation on the server side, so that if you accidentally select the wrong value in the dropdown, this will be reported back to you.

Improvements to PDF export (all species)

Line thicknesses have been increased in the PDF renderer for graph (wiggle) tracks so that they don't disappear.

Retirement of archive 68 (all species)

This release cycle we will be retiring archive 68 (July 2012) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Homologues - export as PhyloXML (all species)

We have added PhyloXML to the list of formats available for exporting Orthologues and Paralogues. Simply select 'PhyloXML' from the dropdown list or format thumbnails when exporting data from the Gene Orthologue or Paralogue pages.

Gene Expression Widget updated (all species)

The gene expression widget has been updated to the latest one.

Colouring of exons in text sequence (all species)

We have changed the colour scheme of our exon text view to help colour-blind users. UTRs are now displayed in dark orange instead of purple, to make them easier to distinguish from the neighbouring translated sequence. You can see an example here:


Marking a region on images (all species)

A new feature to mark a selected region is added to the location, gene and other images. Marking can be applied by drag-selecting a region and then using the zmenu to mark it, or by clicking on a feature on an image and then using the zmenu to mark that feature's location.

New species selector for region comparison config (all species)

The species selector drop-down box on the config page for Region comparison view has been moved to the top of the tracks list. This makes it easier to find the drop-down and thus configuring the species on the view.

Export mode for projectors and print (all species)

To help with the display of Ensembl images on projectors, a new export option, hi-vis, customizes the exported image to be maximally visible on projectors. This link has been added to the standard image export menu.

In this hi-vis image, colours have been gamma-corrected to improve contrast in brightly lit environments and measures have been taken to broaden otherwise very thin lines.

The same parameters have been applied to our print presets, which are now labelled 'Journal' and 'Poster' and produce a x2 and x5 enlargement respectively. More information about outputting for print is available via the help icons in this section of the menu.

As these parameters are tunable, and each situation different, we welcome feedback on the effectiveness of this new feature that we might make it as broadly useful as possible.

Improved Variation Tables (all species)

Variation tables for genes and transcripts have been reimplemented to effectively handle the large number of variants now known for many genes. At the same time, the ability to filter, sort, and select this data has been improved.

Filtering by variant type is now achieved by selecting the "Type:" filter at the top of the main table, rather than by a preceding auxiliary table.

Further features and refinements are expected to be added in forthcoming releases.

Release 81

replace i icon with ? icon (all species)

The "i" icon when clicked gives you the help/documentation page has been replaced with a new "?" icon.

The "i" icon in the tracks configuration has been left unchanged as this is more information rather than help.

Public plugins sqlite and sge_blast removed (all species)

The said two plugins, one for SQLite support for user db and other for SGE BLAST, were outdated and have been removed from the public-plugins repository.

Trackhub settings support (all species)

In this release we have added support for trackhub visibility settings; in other words, tracks that are turned on by default in the hub's trackDb.txt file should automatically be shown in Ensembl.

The only exception is for hubs that we configure internally, such as the Genome Reference Consortium GRIT hub. For these, all tracks will be hidden by default, but you can find them by searching in the Control Panel.

Transcript sequence markup (all species)

Transcript sequences can now be marked up to show exons as alternating upper and lower case characters, rather than grey/blue text. Simply check the "Show exons as alternating upper/lower case" box in the "Configure this page" panel on Transcript cDNA or Transcript Protein pages.

This markup option will also carry over to the sequence export if RTF format is chosen.

Retirement of archives 67 and 59 (all species)

This release cycle we will be retiring archive 67 (May 2012) in accordance with our three-year rolling retirement policy. Due to the arrival of GRCz10 in Ensembl 80 we will also be retiring archive 59 (Aug 2010) which currently shows Zebrafish Zv8 annotation.The data will remain available on our public database server; only the web interfaces will be removed.

User accounts/session database configuration changed (all species)

Database used for user accounts and sesison records was configured using the conf/SiteDefs.pm configurations as below:

$SiteDefs::ENSEMBL_USERDB_TYPE = 'mysql';
$SiteDefs::ENSEMBL_USERDB_NAME = 'ensembl_accounts';
$SiteDefs::ENSEMBL_USERDB_USER = 'mysqluser';
$SiteDefs::ENSEMBL_USERDB_HOST = 'localhost';
$SiteDefs::ENSEMBL_USERDB_PORT = 3306;

These configurations have been removed and now the database is configured by adding configurations in conf/ini-file/MULTI.ini as below:

DATABASE_ACCOUNTS = ensembl_accounts
DATABASE_SESSION = ensembl_accounts

HOST = localhost
PORT = 3306
USER = mysqluser

HOST = localhost
PORT = 3306
USER = mysqluser

Changes to the code can be seen here:

Release 80

Deprecation of Sanger::Graphics (all species)

To improve long-term maintainability of the Perl GD drawing code, in release 79 we moved all necessary functionality from the Sanger::Graphics namespace into EnsEMBL::Draw. All Sanger::Graphics modules have been deprecated as of release 80, and they will be removed in release 82.

This change should only affect developers whose code calls methods directly from Sanger::Graphics instead of inheriting from EnsEMBL::Draw modules.

Note that a few helper modules, including ColourMap, have been moved into EnsEMBL::Draw::Utils.

New web dependency - ensembl-io (all species)

Starting with release 80, the Ensembl webcode will have an additional dependency: ensembl-io, our Git repository for file-parsing code. This can be checked out from GitHub the same way as our other repos, and is also included in the "web" group of repos used by ensembl-git-tools, so that the command

git ensembl --clone web

will automatically clone ensembl-io in addition to existing web code.

Initially this dependency will only affect variation data, but the plan is to integrate the new parsers into other areas of the website such as user uploads. Deprecation of the old parser modules will be announced in due course.

New export options for comparative views (all species)

As part of our ongoing upgrade of the export interface, Release 80 includes the following new features:


Sequence export has been added for both orthologues and paralogues. Unaligned gene sequences can be exported in FASTA format, whilst multiple alignments can be exported in all our usual BioPerl formats (including FASTA); both types can be exported as DNA or amino acids.

Note that at the moment you cannot filter the paralogues by species, as that option is not available within the paralogue page itself.

Gene Trees

Previously, the only export available from individual nodes of the tree was in FASTA and Newick formats. These links have been replaced with one that opens the export interface, so you can choose any of the same formats as the full tree export.

OrthoXML filtering

Exports in orthoXML now honour the current page settings, allowing you to export only the homologues you see.

New styles for BigWig files on karyotype (all species)

Last release we added the ability to display your BigWig data on whole chromosomes or the entire karyotype, as line graphs or histograms. In release 80 we have added two new track styles for line graphs:

1 - "raw mean", i.e. mean values scaled relative to one another, instead of relative to the maximum value in that region (the default setting)

2 - "mean with whiskers", which combines the line graph with "whiskers" to display the minimum and maximum values within each bin.

To use either style, go to the track in the "Configure this page" screen, and choose from the style dropdown.

Gene Expression Atlas Widget (all species)

The Gene Expression Atlas widget has been embedded in ensembl. You can now view where the gene is expressed anatomically (where exactly in the species) and also which experiment it is associated with.


The code has been added to the widgets plugin.

New userdata track type: long-range interactions (all species)

We are very pleased to announce that Ensembl now supports long-range pairwise interaction data, which can be drawn as arcs on Region in Detail. Scores are indicated using a grey-to-black gradient, and labels can be displayed by selecting the appropriate track style from the configuration menu.

Initially we are supporting the two formats developed by WashU for their Epigenomics browser: a simple text-based format which can be pasted into the form or uploaded from your computer, and a richer tabix-indexed format that must be attached via a URL. More information on both formats can be found in our online documentation.

We hope to support more formats in the future, so please let us know which formats you are currently using!

GlyphSets at risk (all species)

The following GlyphSets are unused in the core Ensembl webcode. Third-party integrators should be aware that they are at risk of deletion in a future release. If you have any use for the following GlyphSets, please contact the Ensembl team.

_text, ctcf, fg_wiggle, GlyphSet_feature, histone_modifications, ld2, lsv_variations, missing, P_protdas, P_separator, preliminary, restrict, simple_histogram, tsv_missing, urlfeature, Vrefseqs

Tools (BLAST & BLAT) gap initiation update (all species)

Gap initiation and extension penalties has been updated/changed to reflect the correct order which is dependant on the matrix (BLOSUM and PAM) and the same has been done for BLASTN which is dependant on the match and mismatch score.

Download the ncRNA secondary-structure as SVG (all species)

You can now download the ncRNA secondary structure view as  SVG. A link has been added at the top of the view.

Track label improvements for images (all species)

Some tracks in images now appear within sections, grouping common tracks within a category.

Each section is identified by a heading underlined in a certain colour, and each track within that section by the same colour being used on its left-hand side.

Also, some tracks now have labels within the image itself, to allow particularly long labels. These in-image labels can be configured on or off via the configuration panel.

Initially these features are primarily targeted at trackhub support, but will be increasingly used for other tracks as the opportunity is identified.

Release 79

New CAFE (gene gain/loss) tree View (all species)

We now have a new Gene gain/loss tree view.


The new tree is faster and more interactive than the old tree.  You can also view the tree in a radial or vertical layout (click the double arrow icon on the image blue bar). And you can choose between minimal and full tree (click the tree icon on the image blue bar).

The following browsers support the new view:

IE 9 onwards;  Firefox 31 onwards; Chrome 31 onwards; Safari 5.1 onwards

For older browsers we will continue to show the previous version of the tree.

Moving away from EnsEMBL::Web::TmpFile (all species)

Our old file-handling modules in the EnsEMBL::Web::TmpFile namespace no longer supply all the functionality we need, so we are are in the process of moving to a new set of modules under EnsEMBL::Web::File. These new modules were already in use for the new export interface, but have been substantially expanded in release 79.

Web users should see no change in behaviour, but developers who have been using TmpFile should note that the old modules are now deprecated and will be removed within the next twelve months as we gradually port all file functionality to the new code.

"Download all tables" button has moved (all species)

In line with our other changes to the data export interface, the "Download view as CSV" button on pages with multiple tables has been moved to the main part of the page, above the first table, and renamed "Download all tables as CSV" for clarity.

Individual tables can still be downloaded separately using the Excel icon in the righthand corner of the blue header bar.

Retirement of archive 66 (all species)

This release cycle we will be retiring archive 66 (Feb 2012) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Retirement of Sanger::Graphics modules (all species)

The following is only of relevance to developers who have created custom drawing code for their Ensembl-powered site:

As part of our "under the hood" maintenance of our codebase, we are planning to retire the Sanger::Graphics namespace and move all required functionality into EnsEMBL::Draw. The relevant modules and methods have been copied over, and the old ones will be removed in a future release.

Please note that if your code uses Sanger::Graphics::ColourMap, Bump or TextHelper, these modules have been moved into EnsEMBL::Draw::Utils.

Ensembl search in google search (all species)

There is now a search bar for www.ensembl.org when you get a hit to Ensembl in the results of a google search.

The code has been released but it might take a few days/weeks for google to pickup the changes and to show the search bar in google results.

Regulation matrix tutorial (all species)

You can now close all the tutorial popup in the regulation matrix (in configuration panel) by clicking on the cross icon.

TSL icon on transcript summary page (all species)

We are now showing the transcript support level (TSL) in the summary panel as an icon with a more detailed explanation available when you hover your mouse over it.


DAS Registry removal (all species)

Ensembl releases upto 78 have inspected the DAS Registry for DAS sources that can be attached to the browser. The Registry is being retired in May 2015 and consequently from Release 79 onwards Ensembl will no longer query the Registry. You might notice this as a decrease in the number of sources available via 'Manage Your Data' -> 'Attach DAS'

Removing feature counts on the left navigation (all species)

The feature counts in the left navigation (number in between bracket next to the links) has been removed on all the views and moved to the summary panel (top panel on the summary page).

A new line (About this gene, About this transcript, About this variant, About this structual variant) has been added on the gene summary, transcript summary, variation summary and structural variant summary page which lists the counts.

Query hit distribution image on BLAST/BLAT results page (all species)

A new image view representing the distribution of the HSPs on your query sequence has been added to the BLAST/BLAT results page.

Share BLAST/BLAT/VEP results with others (all species)

Results from Ensembl tools can now be shared with others via URL. The feature is on by default i.e. the tickets can be shared to other by sharing the page's URL, but there is a checkbox in the Ticket List view that allows you to make your ticket non-sharable.

Downloading large VEP results (all species)

Downloading large VEP result text files is now possible.

View BLAST/BLAT results from multiple jobs on location view (all species)

Results from multiple BLAST/BLAT jobs can now be seen simultaneously on location views

Scrollable Region in Detail (all species)

The display within the main panel of Region in Detail can now be dragged using the mouse. To achieve this behaviour, select the 'Drag' icon in the top right hand corner of the image and then use the mouse to drag the display to the right or the left. When you release the mouse button then the image will be reoladed using the new coordinates. To revert to the previous behaviour, where the mouse is used to select a region of the display for navigation, then choose the 'Select' icon in the top right corner of the image

Improved rendering of (Big)Bed features (all species)

Our drawing code has been updated to enable "intron-style" joins within alignment features, e.g. in BED files where these are defined using the blockCount/blockStart/blockSize columns. Select 'Structure' or 'Structure with labels' from the styles menu.

Colouring karyotype "pointers" (all species)

When viewing your own BED files on a karyotype, the drawing code now respects the itemRgb values for each feature, if set.

Display your BigWig files on whole chromosomes (all species)

We have updated our 'Whole genome' and 'Chromosome summary' pages to allow the display of BigWig data across a single chromosome or an entire karyotype. Simply attach your BigWig file through the 'Add your data' interface, then turn on the track in either view. Each wiggle point or histogram bar shows the mean value for that bin (where a bin is 150th of the length of the longest chromosome).

Note that the display across the entire genome will scale according to the maximum value in the entire file, whereas the chromosome display uses the maximum for that chromosome.

Popup userdata menus on karyotype (all species)

The karyotype has been updated with new popup menus for user data. Where features overlap on the genome, the popup menu will show an entry for every feature.

Release 78

Updated export for homologues and trees (all species)

Phase 3 of our export update includes the remaining comparative genomics views, as follows.

Orthologues and Paralogues

Orthologues and paralogues can now be exported as OrthoXML only, using the blue download button above the summary table.

In addition, homologue alignments - both cDNA and protein - are now available in the folllowing formats:

  • Mega
  • MSF
  • Nexus
  • OrthoXML
  • Pfam
  • Phylip
  • PSI
  • Stockholm

To find this export, go to an Orthologue or Paralogue page, click on 'Alignment (protein)' or 'Alignment (cDNA)' in the table and then click on the blue button labelled 'Export alignment'.

Gene trees

The pages 'Gene tree (text)' and 'Gene tree (alignment)' have been removed and replaced with a single export interface. Click on the download icon in the blue bar above the gene tree image to open the export panel.

Available formats:

  • Mega
  • MSF
  • NHX
  • Newick
  • Nexus
  • OrthoXML
  • PhyloXML
  • Pfam
  • Phylip
  • PSI
  • Stockholm
  • Text tree

Gene gain/loss trees

This new option allows you to export gene gain/loss trees in PhyloXML format.

Protein families

Another new export option is the ability to export all the protein alignments for a family. From the Gene Family page, click on a family stable ID and on the following page you will see a blue 'Export family alignment' button above the table of proteins.

Note: this function is only available for families with two or more genes.

Changes to legacy export interface

The PhyloXML and OrthoXML options have been removed from the list on the 'Export Data" popup panel, as they are no longer supported. Please export these formats from the relevant pages.

Removal of obsolete tables from ensembl_website (all species)

The following tables have been dropped from the ensembl_website database as they are no longer in use - their contents were moved to either ensembl_archive or ensembl_production many releases ago:

  • ens_release
  • item_species
  • news_category
  • news_item
  • release_species
  • species

In addition, table help_record_link has been dropped as it was never used - the help_link table is used to associate URLs with help_record entries.

The associated queries have also been removed from EnsEMBL::Web::DBSQL::WebsiteAdaptor.

RNASeq track display (all species)

RNASeq tracks can now be displayed as either a "wiggle track" summary (the default) or as individual features; the summary version uses a BigWig file created from the BAM file. This speeds up the display and allows us to show this information over larger regions than is possible using the raw data.

New speciestree view (all species)

it is now possible to view the ensembl species tree with this new interactive view. In previous release, you only had the possibility to download the tree in pdf but you can now view it here:

http://www.ensembl.org/info/about/species.html  (and click the link "View the full Ensembl species tree")

you can switch between radial and vertical view. You can also view NCBI or Ensembl tree.

The following browsers support the new view:

IE 9 onwards;  firefox 31 onwards; Chrome 31 onwards; Safari 5.1 onwards

And for older browser there will be the link to download the tree in pdf.

Rendering of BigBed files (all species)

We have updated our BigBed parser to reflect changes in the UCSC bedToBigBed script, specifically the naming of the last field as 'chromStarts' in AutoSQL rather than the 'blockStarts' specified in the online documentation.

This allows us to correctly render features that contain this information, i.e. as a series of joined blocks instead of a single alignment.

We have also updated our online documentation about the BED format.

Retitrement of archive 65 (all species)

This release cycle we will be retiring archive 65 (December 2011) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Improved RTF export (all species)

We have now integrated many of the options from the "Configure This Page" interface, e.g. variation filtering, into the RTF export so that any changes you have made to the page will be reflected in your RTF download. You can also change these options in the export interface just before you download, but these changes will not be copied back to the page itself.

Pre Species on the species list page (all species)

We now have a duplicate row for species which is both on pre and ensembl. One row is the species with the ensembl assembly and the row with the faded species image is the one with the pre assembly.


public MySQL server for GRCh37.ensembl.org resources (all species)

The public MySQL server for the GRCh37 databases (ensembldb.ensembl.org port 3337) will contain two full sets of databases - one on the current schema and one on the previous schema.

VEP : quick preview of results (all species)

When pasting compatible data (all formats apart from Pileup) into the input box for VEP you will be presented with a blue 'Quick results for Variant' box. Choosing this will generate a quick preview of the consequences, limited to running the first Variation in the list against the Ensembl Transcript data set. If you wish to view the complete set of results for all Variations in your file then you can still submit the job to our Tools queue as usual.

Release 77

New interface for alignment export (all species)

For Phase 2 of our export upgrade, we have ported the genomic alignment pages to the new export interface. We have also upgraded our version of BioPerl to 1.6.1, which allows us to support the latest write_aln options in Bio::AlignIO. Export file formats supported in release 77 are:

  • Mega
  • MSF
  • Nexus
  • Pfam
  • Phylip
  • PSI
  • RTF (text alignment views only)
  • Stockholm*

This change affects the following pages:

  • Location -> Alignments (image)
  • Location -> Alignments (text)
  • Gene -> Genomic alignments
  • Variation -> Phylogenetic context

The old "Export data" button has been disabled on these pages and replaced with a new button within the page. The Alignments image has a download icon on the toolbar:

and the text-based alignments use the same "Download sequence" button as the pages upgraded in release 76.

* Please note that sites which still use the old BLAST interface have a dependency on BioPerl 1.2.3 and therefore cannot offer Stockholm export

Retitrement of archives 64 (all species)

This release cycle we will be retiring archive 64 (September 2011) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

BioPerl upgrade (all species)

Important: This change only affects developers of Ensembl-powered websites, not general users of our code.

In release 77 we have upgraded to BioPerl 1.6.1 in order to support all the latest features of BIo::AlignIO. This version has long been supported by the Ensembl API, but the old BLAST interface was dependent on features in version 1.2.3 so we were unable to upgrade the web servers until the new interface was released in Ensembl version 76. There are therefore two strategies available to developers:

1. If you are still using the old BLAST interface, do not upgrade to BioPerl 1.6.1. However if you upgrade your site to Ensembl 77, you will need to configure the export interface to use the formats available in the older version of Bio::AlignIO.

Create a file in your plugin with namespace EnsEMBL::Web::Component::DataExport::Alignments and add the following method:

sub alignment_formats {
### Configure this list to match what's available
### in the installed version of BioPerl
  my $self = shift;
  return qw(CLUSTALW FASTA Mega MSF Nexus Pfam Phylip PSI Selex);

2. If you don't use BLAST or have upgraded to the new interface, you should upgrade BioPerl and reconfigure your BioPerl location if it has changed. E.g. if you haven't installed it in /path/to/ensembl/bioperl-live, check in your SiteDefs.pm file for the line:

  $SiteDefs::BIOPERL_DIR                    = '/path/to/bioperl-live';

New icons on transcript table (all species)

Two new icons have been added to the transcript table, showing confidence levels from different projects.

See the following news items for more details on this data:

  • APPRIS tags
  • Transcript Support Levels

Gene expression page has moved (all species)

We have decided to move the Gene Expression table to our per-species documention, as the data is not applicable to every gene. You can now find the list of tissues and associated datasets on the homepage of every species with an RNASeq database, e.g. Homo_sapiens/Info/Expression.

Display of Alternative alleles (all species)

We have added a new Gene panel that shows a table of manually curated alternative alleles. An example of this would be a gene on the human GRCh38 reference assembly and one on a GRC haplotype patch. This table also provides links to Region comparison that are preconfigured to show the regions of interest.

Links between alternative allleles have also been added to Gene Summary panels and to the menus that appear when mousing over a gene on a location view.

Release 76

New BLAST interface (all species)

Ensembl are delighted to announce the release of our new BLAST/BLAT interface, which uses the same Tools infrastructure as the new web-based VEP that came out in release 75.

Highlights include:

  • Tickets saved to a user-friendly table so you can come back later and view or re-run your search
  • Automatic polling of the backend process - no more clicking "Retrieve"!
  • Better error-reporting, so that you can find out more easily why a job failed
  • We now use ncbi-blast instead of wu-blast - this gets around the licensing issues associated with the latter and enables us to distribute our blast code more freely

Please let us know what you think!

Drawing code changing namespace (all species)

As part of our ongoing reorganisation of the webcode git repositories, we have moved all Bio::EnsEMBL drawing code to EnsEMBL::Draw.

This change will affect developers who have created custom drawing code tracks or components that draw images using the DrawableContainer or VDrawableContainer modules. A simple change of namespace in your code will ensure that it continues to work.

Datahub listings (all species)

Ensembl has had support for datahubs (also known as track hubs) for some time, and we have now added a page listing available public hubs for our species. Where appropriate, a link will take you to the sample location for a species and open the control panel so that you can easily configure the hub.

Please note that, particularly with the recent release of human GRCh38, many of these hubs are on old assemblies, so where possible* our links will take you to the most recent archive which included that assembly.

If you have a datahub that you would like including in our registry, please contact us.

* Some assemblies are only available on archives that predate datahub support

Regulation displays (Human)

The display of regulatory regions has been updated to coincide with the release of the data from the new Regulatory build. The major enhancement is a redesigned interface for selecting which types of evidence to display and for which cell types. In addition it allows for easier configuration of how to display that evidence, for example as peaks or as signals.

New Assembly Converter interface (all species)

In addition to the new BLAST interface, we have updated our online Assembly Converter to help our users migrate to GRCh38. The new tool currently uses CrossMap, which means input is limited to the following formats:

  • BED
  • GFF
  • GTF
  • VCF
  • WIG

For more information, see our online documentation on file format specifications.

(CrossMap also supports BigBED and BigWIG, but we are unable to offer upload of large files at the moment. We recommend using CrossMap locally if you have very large datasets to process.)

Initially we are offering this tool only for human assembly mappings GRCh37 -> GRCh38 and NCBI36 -> GRCh38. More species will be added as soon as we have the chain files available.

Important note: CrossMap discards file metadata such as track lines. We are working to implement an updated assembly mapper that preserves metadata, which will be released in a future version of Ensembl.

Retiring of GBrowse format (all species)

In release 76 we will be discontinuing support for the GBrowse file format, as it is little-used, and will be focusing in future on improving support for more popular formats.

New page - news by topic (all species)

In addition to viewing all news for a given release, you can now view all news on a given topic, sorted in reverse chronological order. For example if you want to see all new web features for the last several releases, you can use this link (which also appears on the home page):

All web updates, by release

The following topics are also available:

We hope you find this page useful!

New interface for sequence export (all species)

We are embarking on an upgrade of our Export interface, to make it simpler to use and more directly related to the data you see on screen. The first component to be released is for "text sequence" pages, i.e. views that show DNA or peptide sequence as text.

Features of the new interface:

  • Single interface for FASTA and RTF output
  • Improved support for RTF fonts and background colours in OSX
  • Select "uncompressed" or "gzipped" in the same input form as your other output options, rather than having to click on a second link
  • Uncompressed output can be copied'n'pasted from the file preview or downloaded onto your computer

Note that we have removed the old "HTML" format for FASTA as it was irrelevant in the new interface.


Also, the old "Export data" button has been disabled on pages that use this new interface, to avoid confusion. The old button will be phased out over the next few releases as we upgrade other components and make new export tools available.

Support for VCF format (all species)

Our web interface now supports two types of VCF file. Small files (up to 5MB) can now be uploaded to the website for display by selecting the "VCF" format from the dropdown menu; if you wish to attach a tabix-indexed VCF, please select "VCF (indexed)".

Gencode Track (Human, Mouse)

To have a separate track for Gencode splitting the current Gencode 20 to Gencode 20 comprehensive and Gencode basic. Available for human and mouse only.

Retitrement of archives 62 and 63 (all species)

This release cycle we will be retiring archive 62 (April 2011) and 63 (June 2011), in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Release 75

Gencode Basic Renderer (Human, Mouse)

A new renderer, GENCODE Basics has been added for GENCODE. The GENCODE Basic set comprises only a subset of the transcripts ie. the fragments and other problematic biotypes are excluded from teh basic set.

New VEP interface (all species)

The VEP web interface has been completely overhauled and now offers:

  • new results page with summary charts, interactive filtering and more
  • more options and configuration
  • 750 variant limit removed - limits are now imposed only on uploaded file size
  • VEP now runs on a job submission system

Link from Region in Detail to individual exons (all species)

The popup menu that appears when you click on a transcript now includes a link to the Exon table if you click on an individual exon, and the exon you clicked on is shown in bold on the table. Note that this link will only appear when you are zoomed in enough for the click coordinates to clearly identify a single exon.

Highlighting the current feature (all species)

In Region in detail and similar views, we currently highlight the feature you have come from so that it's easier to find amongst all the tracks. However if you would like to turn off this highlighting, e.g. in order to have a cleaner image to export, you can now do so via the control panel.

You'll find the option under 'Information and decorations', labelled 'Highlight current feature'.

Retirement of archive 61 (all species)

This release cycle we will be retiring archive 61 (Feb 2011), in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Retirement of ensembl-draw (all species)

The ensembl-draw repository has been merged with ensembl-webcode.

The files that were in ensembl-draw can now be found in ensembl-webcode/modules/Sanger/Graphics and ensembl-webcode/modules/Bio/EnsEMBL.

Documentation move (all species)

To aid internal management of git permissions, we will be moving ensembl-webcode/htdocs/info into a separate public plugin, docs. No page URLs will change, but external developers will need to enable this plugin in order to display documentation for the API, etc on an Ensembl-powered website.

ensembl-webcode directory (all species)

Web code is now stored inside the top level directory ensembl-webcode.

A new variable has been added to SiteDefs, called $ENSEMBL_WEBROOT, which has the value of "$ENSEMBL_SERVERROOT/ensembl-webcode", and is used when locating files and directories that are inside ensembl-webcode. $ENSEMBL_SERVERROOT remains unchanged.

Removal of "default action" (all species)

We have removed the web behaviour whereby invalid URLs for genomic views were silently redirected to the default view for that gene/location/etc. This was causing issues with some scripts connecting to the website, including our own selenium testing. Invalid URLs now show a custom 404 component within the standard page template.

Search enhancments (all species)

Ensembl search has a number of improvements including (i) more extensive highlighting of the search term on the results page, (ii) improved ordering of results, and (iii) better handling of non alphanumeric characters in search queries.

Release 74

Species list now exportable (all species)

In response to user requests we have reformatted the Ensembl species page as an exportable table; where relevant the columns are sortable. In addition, we have included taxon IDs and whether or not the species has variation and regulation databases.

ncRNA secondary structure (all species)

We now show secondary structure of non-coding RNAs on the Gene Summary page, using the R2R package.

Example gene

If you click on the 'Enlarge' link, you will be taken to a page that shows a more detailed image of the structure, including base pair annotations.

Note for developers:

If you run an Ensembl mirror and  wish to use this functionality will need to compile R2R on their webserver and then configure the R2R_BIN path in SiteDefs.pm, e.g.

$SiteDefs::R2R_BIN  = '/usr/bin/r2r';

Without these steps, the webcode will omit the SVG image.

Phenotypes from orthologs (all species)

The gene phenotype view will show phenotypes associated with orthologues of the current gene.

Retirement of archive 60 (all species)

In accordance with our archive policy, we will be retiring the Ensembl 60 (Nov 2010) archive when version 74 is released. Release 60 data will still be available from our FTP site and public MySQL database - only the web front end will be retired.

Updated configuration management interface (all species)

You will now be able to share configurations and configuration sets with other users, and with groups you administer.

Configurations and sets from groups you are in will appear in the interface, so you can use them.

You will also see a section called "Suggested Configurations". This contains configurations and sets created by our outreach team, in order to provide a quick and easy means of configuring the site in a number of predefined ways.

The interface can now be found in the Manage Configurations section of the left menu of the Personal Data tab of the popup window, reachable by clicking the Manage your Data button.

Matrix configuration for RNASeq models (Human, Opossum, Sheep)

Configuration for RNASeq models for Human and Opossum now appears as a matrix, in order to more easily manage the large number of tracks available.

SiteDefs rewrite (all species)

SiteDefs has been rewritten so that it no longer exports variables - they MUST now be referenced in other packages with $SiteDefs::VAR_NAME.

$SiteDefs::VERSION has been removed - use $SiteDefs::ENSEMBL_VERSION instead.

$SiteDefs::ENSEMBL_FLAG_NAMES_HR and $SiteDefs::ENSEMBL_FLAG_NAMES have been removed - use $SiteDefs::ENSEMBL_DEBUG_FLAG_NAMES instead.

$SiteDefs::SAMTOOLS_HTTP_PROXY and $SiteDefs::SOAP_PROXY have been replaced by $SiteDefs::HTTP_PROXY.

The following other variables have also been removed, with no replacements:


Release 73

New search engine (all species)

In release 73 we will be switching over to using the Solr search engine, which builds on our existing Lucene search as follows:

  • faceted searching - restrict an existing search by species or category
  • Google-style search listings
  • Highlighting of your search term in results
  • Suggestions of similar terms (in case you mistyped a word)
  • Autocomplete for "real words" (e.g. enzyme names)
  • Preview of top result

Additional enhancements may be introduced in future releases.

Alternative display styles for assembly exceptions (all species)

In order to accommodate the large number of assembly exceptions in Human, we have created alternative display styles for this track on the overview image of the whole chromosome on Location pages.

By default, all exceptions of the same type (e.g. MHC regions) will be collapsed into a single feature, but you will be able to revert to the expanded view using the same controls as other tracks, i.e. the "gear" icon on the blue toolbar, or the popup menu on the track name at the lefthand side of the image.

Database ensembl_website has been split into two (all species)

For better maintenance of our archive system, some of the tables from the database ensembl_website_73 have been moved into a new database, ensembl_archive_73, and the corresponding webcode updated. This change will allow us in future to connect all archive sites via a symlink to a single database with up-to-date information on which other archives are up and running, so that we can link between them.

The new database will be needed if you are setting up a local mirror of Ensembl and wish to link to our archives, but is not otherwise required.

New "Quick Guide" pages (all species)

For release 73 we have added more pages that give short tips on how to use some of Ensembl's most popular features. These pages can be accessed via boxes on the main home page or can be found in the relevant section of 'Help and Documentation'.

New topics include:

Change to EnEMBL::Web::Configuration child modules (all species)

If you use custom versions of EnsEMBL::Web::Configuration::<Object>.pm in your plugins to alter the available components, please be aware that we have made the key "summary" a reserved word*. You will therefore need to change your code as per the following example:

  #change components of the existing Summary node
  my $node = $self->get_node('Summary');
                              summary      EnsEMBL::Web::Component::Gene::GeneSummary
                              transcripts  EnsEMBL::Web::Component::Gene::TranscriptsImage)],


  #change components of the existing Summary node
  my $node = $self->get_node('Summary');
                              gene_summary  EnsEMBL::Web::Component::Gene::GeneSummary
                              transcripts   EnsEMBL::Web::Component::Gene::TranscriptsImage)],

* This was needed in order to configure the chromosome image on Location pages

Release 72

Retirement of archive 58 (all species)

In accordance with our archive policy, we will be retiring the Ensembl 58 (May 2010) archive when version 72 is released. Release 58 data will still be available from our FTP site and public MySQL database - only the web front end will be retired.

Upload your VEP output (all species)

We have added the ability to upload a VEP output file to the website through the standard upload form. This allows you to re-upload previously calculated consequences, whether from a previous run of the VEP online tool that you have deleted from the website, or an output file from the standalone script (subject to our usual 5MB upload limit).

Changes for 'Users' plugin (all species)

In previous release, Users plugin was introduced which was dependent upon the ORM plugin. In this release, Users plugin doesn't need ORM plugin anymore. Thus the given extra declaration can be removed from the Plugins.pm file if Users plugin is being used.

 'EnsEMBL::ORM' => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/orm'

Release 71

New Expression view listing RNASeq data (multiple species)

We have added a new view to the set of gene-based displays, listing the available RNASeq data for that species, with links through to Region in Detail that turn on a set of RNAseq tracks for a given tissue. You can find this page in the lefthand menu on Gene pages, above the Comparative Genomics submenu.

Sample link (Human BRCA2)

We hope this will provide a useful way into the data for users mainly interested in a single gene, but we plan to develop more views in future to allow alternative data selections to be made.

Image resize icon (all species)

We have added an image resize icon (just before the export icon) on the image toolbar for horizontal views. The views can now be resized by clicking the icon and choosing the different sizes (there is also a best fit option).

Note that this is different from resizing the image via the configuration panel where the width get saved to the browser session whereas for icon the size will be reset if you refresh the page.

Scrollable overview image for Region in Detail (all species)

This display is created using javascript, and the HTML5 canvas element and history API, and as such is only supported in modern browsers - up to date versions of Chrome, Firefox, Safari 5.1 and later, and Internet Explorer 10.

If you do not have a compatible browser you will see the static image instead, and there is an option to switch between scrollable and static images for supported browsers.

Transcript comparison view (all species)

You can now view transcript sequences for a gene side by side, with markup for exons and variations. This view is available on gene pages, and can be found from the lefthand menu, below the Splice variants link.

Intron supporting evidence for RNASeq genes (all species)

The RNASeq data supporting the introns of RNASeq genes is now shown on the Supporting evidence panels for those transcripts. The display distinguishes between alignments that support canonical and ones that support non-canonical splice sites.

User accounts code migrated to public plugins (all species)

A new plugin 'users' has been added to the public-plugins containing user login and user groups functionality. Thus the existing code that deals with the user accounts has been removed from ensembl webcode. The user database schema has also been changed, for the existing users accounts to work with the new code, a new script is provided which copies all the existing user data to the new schema. This script is placed in the public-plugins/users/utils/ folder, and contains the essential usage information.

The user plugin requires use of another plugin, placed in public-plugins folder called 'orm' which in turn has a dependency on Rose::DB::Object (on CPAN). Thus for the users plugin to work, Rose must be installed and the plugins file needs to contain two extra declarations above the EnsEMBL::Ensembl declaration.

'EnsEMBL::Users' => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/users',
'EnsEMBL::ORM' => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/orm',
'EnsEMBL::Ensembl' => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/ensembl'

Release 70

Streamlined custom track upload (all species)

We have merged the web interfaces for uploading your data and attaching it via a URL into a single form that changes as you select options. The new interface can be found at the top of the Custom Data menu, under the "Add a Custom Track" link.

We hope this will make it simpler to create custom tracks from any kind of file.

Video embedding: YouTube vs Youku (all species)

For the convenience of our Chinese users, we now automatically use the Youku versions of our video tutorials instead of the YouTube ones if you visit any of our sites from a Chinese IP address.

Automated compara documentation (all species)

In recent releases, documentation of pairwise alignments has been generated using Perl scripts as part of the compara pipeline. This created dozens of HTML files and images, which all had to be committed to the web code every release.

We have now transferred most of this content into modules under EnsEMBL::Web::Document::HTML. Not only does this ensure that the documentation is always in sync with the database, but it will allow other Ensembl-powered sites to create their own compara documentation with minimal work, as lists of species are retrieved from the compara database and all configuration is done automatically using web parameters.

Matrix configuration for datahubs (all species)

Track for datahubs with dimensions will now be configurable via a matrix.

Retiring archive 57 (all species)

Ensembl archive 57 is retired (both database and website).

Release 69

New species homepages (all species)

Following on from last release's design changes, we have revamped the homepages for individual species (e.g. Human) to incorporate lots of links to our content in a crisp, clear layout. The previous text content is still available, via the "More..." links in the assembly and genebuild sections.

We hope that these changes make it easier for you to find Ensembl content quickly!

New Species Tree (all species)

A new view (Gene Gain/Loss tree) has been added under the compara menu on the Gene page, to display the new gene trees produced using CAFE.

Improved Gene tree legend (all species)

Gene Tree legend has been improved to make it clearer and less confusing.

Headers have been added to each column and the alignments legend have been splitted into two (collapsed alignments and expanded alignments) with bigger symbol.

Extra spacing added in between the legends to make it clearer.

New display: Scrollable Region (all species)

There is now a dynamic version of our location view, called "Scrollable region" in the left hand menu.

This display is created using javascript and the HTML5 canvas element, and as such is only supported in modern browsers - up to date versions of Chrome, Firefox, and Internet Explorer 9 and later. There is also support for Safari 5.1, this doesn't always work on certain old Macbooks. If you have any problems, please change to one of the other browsers.

New display: All Phenotypes (Human)

We have a new display for species with phenotype data (currently only human) which lists all available phenotypes in alphabetical order. In due course we hope to have a more comprehensive page displaying phenotype ontologies, but in the meantime this should help you to explore the wide variety of phenotypes available within Ensembl variation data.

The new page is accessible from the lefthand menu on any phenotype location page.

Release 68

Species aliases in URLs (all species)

The Ensembl webcode now incorporates the species.alias array from the meta table in the core database, and therefore accepts any of these values as a species URL. For example, you can reach the Ensembl Human homepage with any of the following URLs:

This change should make it easier for external websites to programmatically generate valid links to our pages.

Web design refresh (all species)

Starting with release 68, we will be incrementally refreshing the design of the Ensembl web template to improve its usability and make it easier to find the information you need.

The first stage involves minimal changes: a new icon set and tweaks to the page layout, designed to make the pages tidier, more consistent in appearance and therefore more readable, without altering current functionality. The only substantial change is the replacement of the "export image" button with a toolbar giving access to common functions like track configuration, data upload and image export.

Subsequent changes will be user-tested before rolling out, and will be previewable on our beta site at beta.ensembl.org. We will also be updating the underlying HTML and CSS to ensure that it works optimally with the current generation of browsers.

These changes will mainly impact developers of Ensembl-based sites who customise the page templates. The new icons are provided in both black and white versions for use on a variety of backgrounds, and we have made some minor changes to our colour schemes. If you have any questions about implementing the new look'n'feel, please do contact us on our developers' mailing list: dev@ensembl.org

Retiring archive 53 (March 2009) (all species)


The archive 46 and 53 versions of Ensembl will be retired as part of this release.

As a result, aug2007.archive.ensembl.org and mar2009.archive.ensembl.org will no longer be accessible.


Soft masked index files for BLAST and BLAT (all species)

We are switching to soft-masked genomic DNA rather than unmasked genomic DNA as the data source used when generating our search index files for BLAT. A BLAT search from release 68 onwards will automatically search against a soft-masked genomic sequence  We will also add an option to search against a soft-masked database for BLAST in addition to the unmasked and hard masked genomic databases we have previously provided.

Renamed web-code modules (all species)

Several of the modules used to display variation data on gene, location and lrg pages have been renamed. The list of modules affected is below, (old name >>> new name):


Component/Gene/GeneSNPTable.pm >>> Component/Gene/VariationTable.pm
Component/Gene/GeneSNPImage.pm >>> Component/Gene/VariationImage.pm
Component/Gene/SpliceImage.pm >>> Component/Gene/SpliceImage.pm
Component/Transcript/SNPView.pm >>> Component/Transcript/PopulationImage.pm
Component/Transcript/TranscriptSNPTable.pm >>> Component/Transcript/PopulationTable.pm
Component/Transcript/SNPTable.pm >>> Component/Transcript/VariationTable.pm
Component/LRG/LRGSNPTable.pm >>> Component/LRG/VariationTable.p,
ViewConfig/Gene/GeneSNPTable.pm >>> ViewConfig/Gene/VariationTable.pm
ViewConfig/Gene/GeneSNPImage.pm >>> ViewConfig/Gene/VariationImage.pm
ViewConfig/Gene/GeneSpliceView.pm >>> ViewConfig/Gene/SpliceImage.pm
ViewConfig/Transcript/SNPview.pm    >>> ViewConfig/Transcript/PopulationImage.pm
ViewConfig/Transcript/TranscriptSNPTable.pm >>> ViewConfig/Transcript/PopulationTable.pm
ViewConfig/Transcript/SNPTable.pm >>> ViewConfig/Transcript/VariationTable.pm
ViewConfig/LRG/LRGSNPTable,pm >>> ViewConfig/LRG/VariationTable.pm
ImageConfig/TranscriptSNPView.pm >>> ImageConfig/transcript_population.pm
ImageConfig/GeneSNPView.pm >>> ImageConfig/gene_variation.pm
ImageConfig/GeneSpliceView.pm >>> ImageConfig/gene_splice.pm

New variation image page on transcript tab. (all species)

For species with a variation database there is now a new page 'Variation Image' on the transcript tab. This displays a cut down version of the 'Variation Image' from the gene tab, showing data only for the transcript you are currently looking at.

Release 67

Multi-species view renamed (all species)

The page "Multi-species view" will be renamed "Region comparison", to reflect the fact that you can now align regions within a species as well as across species.

Patch alignments (Human)

Alignments between the reference genome and patches are now viewable in Region Comparison. These are currently only configurable by starting from a patch location; click on the 'Select species or regions' button in the left-hand menu and choose 'Human' from the list of species:

Example region in human (chromosome 1, patch HG989)

Data is currently available for human only, but mouse patches are expected in future releases.

Search lucene server variables moved (all species)

Move the search lucene variables (LUCENE_ENDPOINT, LUCENE_EXT_ENDPOINT and others....) from DEFAULTS.INI to SiteDefs.pm in all plugins.

Sequence track on by default at high zoom levels (all species)

The DNA sequence track now turns on automatically when you zoom in to 1000 basepairs or less. Note however that if you turn it off manually, it stays turned off; you will have to turn it back on manually to display it.

Additions to variation popup menus (all species)

When you click on a SNP in Region in Detail, the popup menu now includes links to Population and Phenotype pages if this data is available for the variation.

Release 66

Region Report Tool (all species)

The Region Report API script can now be run through a web interface that allows you to upload a list of regions to be exported. Click on the "Manage Your Data" button - you'll find the Region Report tool at the bottom of the "Data Converters" menu.

We have limited the upload to 5MB for larger features such as genes and 1MB for small dense features such as variations, to avoid overloading our servers, but hope that this will provide a useful feature for simple data analysis. Output is available as either GFF3 or our own text format.

Consequence type filter for variations on sequence views (all species)

There is now an option to filter by variation consequence type on sequence views. Go to configure this page, and select one or more consequence types to filter by (note that you have to turn variations on separately)

Patch alignments on Multi-species view (Human)

You can now view alignments between patches and the reference sequence in Multi-species view for Human. Navigate to the region of a patch and select it from the species selector.

Legend on gene summary (all species)

Legend on gene summary is now available and can be added/removed from the configuration panel.




If you have a copy of ensembl_web_user_db, there is a new column in the configuration_details table. There is a script - utils/update_config_details.pl - which will alter the table and populate the new column correctly.

You MUST populate the column, or else any existing configurations will be inaccessible.

Release 65

Segmentation Features (Human)

Displaying segmentation track for the functional genomic display.  Also available on the location and gene display.

Saving configurataions (all species)

You can now save configurations by clicking the "Save as..." button below the navigation menu when configuring a page.

Saved configurations can be activated by going to the "Manage Configurations" tab, or using the "Load configurations" button.


You can also group configurations from across the site into sets, to make it possible to activate them all at once.

Manage data interface changes (all species)

The Manage data interface has been given an overhaul to improve consistency of display and functionality (sharing, saving, renaming, deleting) across all sources of data.

Adding custom data (all species)

When you add data to Ensembl, it is now only turned on for the page you are currently using, rather than for all pages on the site.

Release 64

User data on Multi-species view (all species)

User data is now viewable on Multi-species view

Configuration panel improvements (all species)

A number of changes have been made to the display of the configuration panel (accessed via the "Configure this page" button), including a new menu structure with grouping for similar track types

Configuring supporting evidence for regulatory features (all species)

Configuration for regulatory evidence is now accessible via two links in the Regulation section of the menu for the configuration panel - "Open chromatin & TFBS" and "Histones & polymerases".

From these links you can access a matrix to choose cell line and evidence type options, as well as changing the renderer for the tracks. These tracks are no longer accessible from other sections of regulation configuration.


Auto-resizing images (all species)

If you set image width to be "best fit", the images will now resize to fit inside the browser window when it is resized

Release 63

Uploading zipped files (all species)

Upload of custom data (BED, GFF, etc) now supports both .zip and .gz formats seamlessly. Files are unzipped during uploading and stored on our servers in uncompressed format.

Lucene plugin (all species)

Our plugin for the Lucene search engine has been made public. Please note that this is only the web interface - it requires a Lucene web service to connect to. We intend to provide instructions on how to set up your own Lucene server in a future release.

The main web code for simple text-based searching (UniSearch) has also been refactored, and old code removed. This should make it much easier to develop additional plugins for other search engines - see the lucene plugin for the modules you will need to create.

Sortable tracks on images (all species)

Tracks on Region in detail and Region overview pages can now be reordered by dragging them to a new position on the image.

There is also an interface for this in the control panel, which is available on the following additional views:

  • Location: Alignments (image), Multi-species view
  • Gene: Summary, Regulation
  • Regulation: Feature context
  • Variation: Genomic context

Favourite tracks saved across all configurations (all species)

If you make a track your favourite on one page, it will be marked as a favourite on all pages where it appears.

Download genotype information as CSV (all species)

The download view as csv has been enabled for the individual genotype information. The tables can now be downloaded as CSV format.


Tracks on location based Multi-species and Alignments (image) views are now configurable on a species by species basis (all species)

There is now a dropdown with a species list in the configuration panel for these pages. Only tracks for the selected species will be displayed, to make configuration easier.


On Multi-species view, there is an All species option, which contains options for which alignments to show.

Species selection on Multi-species view is saved (all species)

Your choice of secondary species is saved for each primary species so that when you come back to the site you don't have to make the selection again.

New style popup menus on images (all species)

The menus which appear when you click on tracks on images (e.g. Region in detail) have been redesigned.

New style regulation configuration matrix (all species)

The Evidence types matrix has been redesigned so that it fits more easily in the configuration panel.


The checkboxes have been replaced with a grid, with colours indicating the status of the options - light blue for off, dark blue for on, grey for unavailable.


Options can be changed by clicking on the grid, and there is also the ability to select or deselect all options in a column or row from a menu which appears when hovering over the labels for that column or row.


Additionally, selection can be performed by holding down the left mouse button and dragging over the grid, but note that this performs a toggle operation, so any options in your selection which were on will be turned off, and vice versa. (This functionality is not available in IE 8 and older.)


Finally, there is a filter input, allowing for quick identification of required options.

Download as CSV button on tables (all species)

Most tables on the site now have a button to download the data as a CSV file in the table header (to the right of the filter).


If you hover over the button you will get a popup with options to download the entire table, or just the data visible at the time. Clicking on the button without waiting for this popup will download the visible data.

Probe features in gff export (all species)

Probe features are now included in the export for GFF Format.

Release 62

Support for BigWig format (all species)

In addition to BAM format, the Ensembl website now supports attachment of BigWig data via URL. Click on "Manage Your Data" then select "Attach Remote File" from the lefthand menu.

Export on Karyotype (all species)

Will try to get the karyotype exported to PDF and other formats. Export button just below the karyotype image

BED Format export (all species)

Adding BED format to the export functionality on location, genes, transcript and variation.

Highlighting row in feature table for variation (all species)

When clicking on a SNP on the karyotype for phenotype, the corresponding row (variation) is highlighted in the feature table

Line numbers on exon view (all species)

Line numbering can now be added to exon sequence when configuring the exon view page

Resizable control panel (all species)

The control panel which appears for page configurations, exports, etc. can now be resized and moved around the page

Searchable content (all species)

The ensembl search now includes content from the Help database and from static content pages, for example species homepages.

Supporting Evidence (all species)

Supporting Evidence View, ie the view that shows the alignments of transcripts/exons and evidence, is now configurable.

Release 61

Favourite tracks (all species)

You can now use the star icon in the configuration panel (accessed via the Configure this page button below the left navigation menu) to mark tracks as favourites.

These can then be displayed together by clicking the 'Favourite tracks' link in the panel's navigation menu.

***IMPORTANT FOR DEVELOPERS*** Schema change to session_record table (all species)

There has been a schema change to the session_record table in the ensembl_web_user_db database.


As we do not provide dumps of this database, you MUST run the script /utils/update_session_record.pl when updating to the new code for this release, otherwise track configuration will no longer be stored correctly. This script both alters the table and updates all existing configurations to work with the new code.


Further changes to this table will probably be coming over the next few releases. You will be notified here in cases where an action is required.

New popups on images (all species)

Configurable tracks now generate a popup when hovering over the track name. This popup provides an easy way to change the track's renderer or remove it from the image without having to go to the configuration panel. The popup also provides information about the track.

'Did you know...' box is back (all species)

The 'Did you know' box on the home page is back. It displays tweets of ensembl. This has been implemented with the New Twitter API. New cpan module installed Net::Twitter.

Static server (all species)

Ensembl can now serve static files - images, css and javascript - from a different URL, specified in SiteDefs as $ENSEMBL_STATIC_SERVER.

This change reduces server load as cookies will not be registered for the static domain.

If no ENSEMBL_STATIC_SERVER variable is set, the site will behave as it did previously.


Changes to ZMenu plugins (all species)

ZMenu plugins now work in the same way as the rest of the code.

Previously all modules matching the required namespace would be called, starting from the most important plugin and ending with the core code.

Now only the first matching namespace will be used, and as a result plugin code should be changed to call $self->SUPER::content in the content function where required.

Release 60

Large scale changes to webcode (all species)

There are a number of changes to how web pages are configured and rendered which will affect plugin developers, most notably to EnsEMBL::Web::Configuration and EnsEMBL::Web::Document::HTML modules, and $SiteDefs::OBJECT_TO_SCRIPT

See here for full details.

Autocomplete Gene searching on Location pages (all species)

The navigation bar on location pages has been changed. Locations can now be typed in one input box, rather than three, and there is a new input to search for genes.

This new box features an autocomplete dropdown for all genes with xref display labels, and will take you to the location of the gene you searched for.

History and Bookmarks in tabs (all species)

When you are logged in, recent browsing history is stored on dropdowns accessible from the tabs in the header of the website (up to 5 links per tab). Up to 5 bookmarks are also available from these dropdowns, ordered by most frequently used.


There is also a dropdown from the species tab, providing quick access to all species home pages. This is available even if you are not logged in.

Gene Ontology view (all species)

The Gene Ontology page on the Transcript page has changed. Instead there is now a Gene Ontology sub-menu with an Ontology Image and an Ontology Table.

The image visualises the term graph of Go terms and the terms closest in the goslim and goa subset for cellular_component, biological_process and molecular_function.

The table lists the go terms for forcellular_component, biological_process and molecular_function and thier closes term(s) in the goslim and goa subset.


Both new pages make use of the Ontology API, and the Ontology image uses EnsEMBL::Web::Tools::OntologyVisualisation. In principle this could be used with any OBO ontology.


Download as CSV (all species)

Pages with tabulated data now have a "Download view as CSV" button at the bottom of the left hand menu. These files can be opened in Excel or other spreadsheet programs.

Upgrade to Gene - Variation Table page (all species)

The Variation Table page has been redesigned to cope with the large amounts of data it can display.

Initially you will see a summary table of available consequence types, and clicking on the "Show" links here will display additional tables with information about the relevant variations.

RNA-Seq data on location views (all species)

RNA-seq data supporting the introns for RNA Seq genes can be rendered with the height of the features scaled according to the read coverage (upto a maximum of 50).

New web page - Multi/GeneTree (all species)

In order that external sites can link directly to Ensembl on a gene tree stable ID, we have created a new view that does just that. It uses the same image code as the genetree for a specific gene, but with all nodes expanded.

Sample link: http://www.ensembl.org/Multi/GeneTree/Image?gt=ENSGT00590000083062

Assembly and genebuild information on archive links (all species)

On species-specific pages, the "View in archive site" panel (accessible from the footer of every page) now shows assembly and genebuild information for each archive, to make it easier to choose the right archive.

Structural Variation tab (Dog, Human, Mouse, Pig)

Structural variations are now displayed in their own tab.Currently this dispays a context iamge and tables of overlapping features. The number of available view for this feature type will be extended in release 61

Release 59

Changelog (all species)

As of release 59, Ensembl will use a changelog to track detailed updates to the data and code. This will be separate from the release news, which will focus on major updates such as new species and web features.

The changelog is stored in the new ensembl_production database, rather than ensembl_website.

Public plugins (all species)

We are overhauling public-plugins/admin, as it is very out of date. This will probably affect very few users, but for those that do use it, there will be quite a few changes in the next couple of releases so we wanted to give plenty of notice!

Firstly, we are creating a new public plugin, 'orm', which will reduce and ultimately remove our reliance on Class::DBI::Sweet by replacing it with Rose::DB::Object. Access to non-essential web functionality, including user accounts, will be ported to this plugin over the coming releases. This plugin will also be a requirement for the admin plugin, since the new CRUD interface uses Rose for its ORM (object relational mapping) component.

Note that the core web code (in /modules) is in the process of being changed to use DBI directly for access to the ensembl_website database, for example for help and news. This is so that simple mirror sites do not need to install the Rose ORM suite and all its dependencies.

If you have any questions, please email us at dev@ensembl.org.

Removal of Object::Help (all species)

The module EnsEMBL::Web::Object::Help and its associated Factory, as well as the EnsEMBL::Web::Data classes for help records, have been removed from the web code, as they were no longer needed. If you have any custom modules in the Help namespace (e.g. Components), please change them to use Hub. See for example EnsEMBL::Web::Component::Help::View for examples of how to substitute 'hub' for 'object' and how to get data from the ensembl_website database using DBSQL::WebsiteAdaptor (you may need to extend the adaptor in your plugin).

Key and Zmenu for Xref (all species)

The xref display and description is now fixed on the vertical drawing (whole genome), now showing the exact xref and associated gene. Also a key has been added to describe which pointer is which. And finally the Zmenu is now working properly describing the gene and xref accordingly.

Future Plans

Read about our future plans on our blog!