πŸŽ‰ BlueGenes 1.0.0 release πŸŽ‰

We are super excited to announce that BlueGenes 1.0.0 has been officially released!

BlueGenes is a new user interface to InterMine utilising its extensive web services combined with a modern web application stack, to provide a more interactive experience for exploring and analysing your data. In contrast with the previous interface, BlueGenes is separate from the InterMine server, increasing the ease of further development to both.

The new interface provides the same feature set you’re already familiar with, wrapped in a new design offering an enhanced user experience. In addition, it allows you to quickly change the InterMine server you’re connected to, to any other instance in your organisation or that is available through the InterMine Registry. While the old webapp acted as a front-end to a single InterMine, BlueGenes can be configured to serve multiple InterMine servers.

A new Tool API for adding custom visualisations and analyses tools to your InterMine has also been introduced. This allows you to create your own tiny JavaScript apps (or adapt the ones we have developed for HumanMine and FlyMine) for your InterMine data, which BlueGenes will display for list analysis, query results and/or report pages, depending on what you specify it supports.

While this is the first major release, we still have lots more coming. Some admin tasks, notably creating templates, is not available in BlueGenes yet so you will have to access the legacy webapp for this. The web services have yet to be separated from the legacy webapp, so it will continue to be available for a while (if you wish to wait with switching to BlueGenes, we recommend using the latest InterMine 4.x release instead).

This new release requires InterMine 5.0.0. To upgrade to InterMine 5.0.0 please read the upgrade instructions carefully.

InterMine 5.0.0 release

This releases contains new web services to support BlueGenes’s new features, in particular:

  • Login using OAuth2 (e.g. Google, Elixir)
  • Upgrading lists
  • Generate external links
  • Submit feedback
  • Reset password

This release includes the Frictionless Data Package specifications implemented by Nikhil Vats. Please see the documentation here for more details.

All the InterMine artifacts have been published on the Maven Central repo instead of Bintray’s JCenter due to the recent jcenter/bintray shutdown announcement.

For more details about this release, please see the release notes.

Documentation

The user documentation has been adapted to the new interface by Hanan (Outreachy intern) and is available here.

The InterMine Server documentation (aka dev documentation) has been revised by Mardhiyah (Outreachy intern) and is available here.

FlyMine and HumanMine

FlyMine has been updated to use BlueGenes. If you use Firefox, you might experience an issue due to the browser cache, in that case you need to delete the cache. The legacy user interfaces is still available here.

HumanMine will be updated soon.

Thanks to …

… all our users/contributors for their support, feedback and help. Thanks to Joshua Heimbach and Yo Yehudi for their great and essential past contributions to this project. Thanks to our excellent interns who have directly contributed to BlueGenes; Akshat for the 2019 GSoC project Javascript Data Visualisations, Sakshi Srivastava for the 2020 Outreachy mid-year project Javascript Data Visualisations, Roshni Prajapati for the 2020 Outreachy mid-year project Improve UI & UX of BlueGenes, and Hanan Younes for the 2020 Outreachy end of year project Create InterMine user training docs.

Contact us

If you have any questions or concerns about any of these changes, please do not hesitate to contact us.

InterMine 4.3.0 release

We are pleased to announce the new InterMine release 4.3.0.
It includes a few improvements and bug fixes.
This is a non-disruptive release.

Improvements and bug fixes

  1. Added a new generic obo source which can be configured in project.xml (Sam Hokin)
  2. Removed the gretty plugin from testmine which now uses gradle 4.9
  3. Removed duplication of so.obo file
  4. Fixed the Google Charts API which broke various things, including the humanmine expression viewers
  5. Updated Google auth and userinfo endopoints
  6. Fixed the NullPointerException in the report page caused by an empty value in the field key used to generate the permanent URI (Share button)
  7. Fixed the home page loading when bioschemas markup are enabled (markup.webpages.enable=true) and JAVA 11 is used
  8. Fixed the webservice query/results when the format is jsonobjects and the root class is a simple object – with no id (Sam Hokin)

See release notes for detailed information.

Upcoming releases

For more information about the upcoming releases, please visit the InterMine roadmap here.

BlueGenes 0.10.0 release

This release was made to coincide with the InterMine 4.2.0 release, which included many updates to webservices important to BlueGenes. While BlueGenes aims to retain backward compatibility with InterMine instances all the way back to API version 27, (appropriate messages are displayed if your instance doesn’t support a feature) many new features are dependent on being up-to-date with InterMine releases.

We are still working towards the production release of BlueGenes, at which point we can recommend it for future deployments over the legacy user interface. This recent year has brought with it a plethora of necessary technical improvements and bug fixes, along with new additions to bring the user interface towards feature parity with the current webapp. The following details the most visible changes to BlueGenes in the last release, which you can explore by updating your local instance or using the public BlueGenes instance.

Visualization tools

  • New version of Tool API to allow list and query results page tools that use IDs from multiple classes
  • Tools on list and query results page should work properly for all classes now
  • Tools on list and query results page now update when editing im-table
  • Initialisation of tools has been made more performant
  • CovidMine visualization for Cases

im-tables

  • Better selection of constraint operation when creating filter
  • Filter manager for adding and modifying constraints and logic
  • Overly wide table contents are now hidden behind a scrollbar
  • Helpful messages and options when something goes wrong
  • Histogram in numeric column summary has been fixed and more features added
  • Calendar for Date type constraints
  • Searchable dropdown for single and multiple value constraints

Query builder page

  • Build queries with outer join and sorting
  • Save queries to your account
  • Load recently run queries from your current session
  • Data browser for selecting the root class
  • Import query from XML

Profile page (new)

  • Change your password or preferences
  • Delete your account
  • Register a new account for a mine

Lists

  • Folder hierarchy for your lists in My Data
  • Add and edit list descriptions

Interactive tool store

  • Currently placed in the developer page, but we intend to move it to an admin page in the future
  • Manage the installation, updating and removal of BlueGenes visualization tools using a web interface
  • Rich information on each tool, where they’ll be visible, and any compatibility issues with the currently active mine
  • All Tool API compliant npm packages with the bluegenes-intermine-tool tag are shown (only tools under the @intermine scope are installed by default)
  • Only superusers are allowed to make changes

Report page

  • Show FASTA information on report page when available (we intend to make drastic changes to the current report page in the near future)

Technical

  • Much improved handling of mines that are unresponsive or have erroneous web services
  • Java 11 support and a docker container

Previous minor releases

There have been some notable changes in prior minor releases. As they haven’t been mentioned in a blog post, we will include them here.

  • Dynamic page titles (the text displayed in the tab or window title) based on the current page and its contents
  • Improvements to the keyword search page
    • Filters should work as expected when applied
    • Multiple filter support
    • Endlessly display more results by scrolling down
    • Restoration of scroll position when returning to search page
  • Reworked routing
    • New and improved URL paths
    • Deep linking to pages of specific mines
  • Stability improvements to mine switching and initialising
  • HTTPS support

InterMine 4.2.0 release

We are pleased to announce the new InterMine release 4.2.0.
It includes new functionalities to support the upcoming BlueGenes release 0.10.0, some improvementes on FAIR side and a few bugs fixes.
This is a non-disruptive release.
Thank you so much to our contributors: Ahmed Hafez, Asher Pasha and Sam Hokin!

BlueGenes related improvements

  1. Added /login web service that merges the anonymous session with the user logged in.
  2. Added /logout web service.
  3. Added a new webservice to change the users’s password.
  4. Updated the existing /lists webservice which allows modifying the list description.
  5. Improvements on the Date type (to support CovidMine).

BlueGenes 0.10.0 will be released soon and announced in a separate blog.

FAIR related improvements

  1. Simplified the webservice that generates Bioschemas markup for the report page.
  2. Adopted DataRecord in the report page.
  3. Added Gene, Protein markup in the report page.
  4. Added BioChemEntity markup in the report page (only if configured).
  5. Added the ontology licences to the obo converters.

Bug Fixes / Improvements

  1. Added a new bio source to load ISA files in json format
  2. Fixed organism short name generation (Ahmed Hafez)
  3. Fixed a bug related to long fields in the report page (Asher Pasha)
  4. Removed BioEntity.ontologyAnnotations because redundant (Sam Hokin)
  5. Fixed src.data.dir.include (gff3 and xml) ans src.data.dir (intermine-items-xml-file)
  6. UniProtFastaLoader works with organism names longer than 2 words (for example Severe acute respiratory syndrome coronavirus 2)

See release notes for detailed information.

Upcoming releases

For more information about the upcoming releases, please visit the InterMine Development Roadmap. More details on the roadmap here.

New FlyMine build: FlyMine 49, now with added JBrowse!

FlyMine has been updated to the latest version of FlyBase. All other data sets have also been updated to the newest versions, we have fixed a few bugs and made the JBrowse displayer available again. See the data sources page for a full list of the current datasets and their versions.

All data can be accessed through our comprehensive library of template searches or by building your own queries using the query builder.

If you have any questions, please see our docs and do not hesitate
to contact us should you require any further assistance. For help and
feedback please email support@intermine.org or visit our contact page.

[Post originally drafted by Sergio Contrino]