Latest version - 1.10.3
Please see Getting SEEK for details about installing SEEK
If you have any comments or feedback about a release, then please Contact Us
Release date: 30th October 2020
This version includes the following bugfixes:
- Fix to the external search over BioModels
- Fixes to doing a search over filtered results, and maintaining the correct order from the search results
- Adding new version comments for Documents
- Fix to Dataset schema.org markup
Release date: 28th August 2020
This version includes a few bugfixes:
- A fix to a validation error when linking to a older publication with no publication type defined.
- A fix to adding via a URL, where the remote server doesn’t respond to HEAD requests.
- Better handling of when the attr_encrypted key is missing or wrong, which previously prevented the server starting up.
- A fix to activity reporting, where a snapshot pointed to a deleted resource.
Release date: 24th June 2020
This version contains a few bug fixes and security updates, and minor feature additions. In particular:
- Rails upgrade to the latest Rails 5 release (126.96.36.199), along with some other dependencies
- Discussion links now have an optional label, to be displayed instead of the raw URL
- Discussion links are now included in the API
- Model organism has been included in the API
- The Model image link has been included in the API
- An improvement to how Submitter and Other creators are displayed, to be less ambiguous
- Request resource has now been entirely replaced by the improved ability to request contact
- A fix to a bug that prevented Assays and Assets being unlinked, if there was only 1 Assay
Release date: 9th June 2020
- Filtered search and browsing:
- When viewing index page lists, it is now possible to change the sort order, and filter by certain attributes
- It is also possible to perform a text search over the list, and apply filters to the results
- Filters across categories have AND applied, whereas within a category OR is applied
- Enhanced support for publications:
- Support for more publication types, including: Journal article, inproceedings, inbook, etc. Users can update the publication type when editing the publication.
- Additional metadata attributes including booktitle, editor, publisher, a remote URL
- For publications, which are manually registered or imported from bibtex files, users can edit all fields of publications.
- For publications registered with DOI, users can refresh the metadata by clicking “edit publication”
- Improvements to importing publications by a bibtex file
- Ability to import different types of publications
- Add more validations to support different types of publications
- Generate the citation according to the type of publications when there is no DOI or Pubmed ID
- Adding one or more Discussion Channel links to all Assets
- If you wish to provide the ability to open a discussion about an item, one or more links can be added to locations such as Slack, GitHub issue, a Forum thread
- A “Request Contact” button for Assets, to allow a registered user to initiate an email discussion with the owner and creators of that item.
- Increased zoom level when previewing model images, and ability to view the original in its full resolution
- Support for ‘include’ when using the JSON API
- Allows you to get full details about related resources in a single call ( see JSONAPI specification)
- For example https://fairdomhub.org/projects/19.json?include=people expands information about the people in an included block at the end of the top level JSON.
- Study Experimentalists attribute has been deprecated - existing entries aren’t lost and can be edited, but the attribute has been removed for new entries or existing entries where that attribute hasn’t been set
- Renaming of contributor to submitter - to be clearer about what this attribute represents
- Update of BiVeS - used for model version comparisons, has been updated to the latest available version
There have also been many other minor bug fixes and improvements.
Note that with this version, we moved from JIRA to Github Issues, and for this and probably future versions have stopped providing links to individual tasks.
Release date: 17th October 2019
- Minor User Interface improvements
- More consistent sorting of lists.
- Consistent Add New button to add new items linked to the current item. This replaces buttons that only appeared in some places - such as the “Add New Data File” for “Assay”.
- Split Edit and Manage action between 2 separate pages, rather than being handled through the same form.
- Initial support for bioschemas.org / schema.org JSON-LD markup
- Supporting Project, Taxon, Sample, Event, DataSet, DataCatalogue, DigitalDocument, and PresentationDigitalDocument
- Validating assay and technology type URI’s (particularly when submitting through the API).
- Managing project members through the API.
- Fix to an problem and inconsistency with how countries and the country codes are stored and displayed
There have also been several minor bug fixes and improvements, which are described more within the SEEK v1.9.1 release notes
Release date: 16th July 2019
- Major upgrade of the underlying platform
- Rails 4.2 → Rails 5.2
- Updating and replacing affected libraries and dependencies
- A lot of bugfixes and minor improvements discovered during the upgrade testing
- Ability to login with email as well as username
- Ability to edit previous version revision comments
- Show the SEEK ID of the selected node when navigating the ISA overview
- Fix for model files appearing missing for previous versions (don’t worry, no files were actually lost)
Changes are also described in the SEEK v1.9.0 release notes. Please note that many of the bugfixes are those created during the Rails upgrade, due to changes in the Rails version.
Release date: 29th May 2019
Bug fix release:
- Fix to correctly clean up permissions when a contributor is deleted
- Additional constraints to prevent invalid permissions, particularly when changing through the API
- Fix to finding related Organisms to a Sample through an NCBI ID attribute
Changes are also described in the SEEK v1.8.3 release notes
Release date: 25th April 2019
Bug fixes and minor improvements, changes are:
- Fix to a potential database lock, particularly when registering multiple items in quick succession through the API
- Ability to edit version revision comments
- Fix to correctly show the creator of a particular DataFile version
Changes are also described in the SEEK v1.8.2 release notes
Release date: 18th March 2019
Bug fixes and minor improvements, main fixes are:
- Fix to some cases where the RDF wasn’t including associated assets
- Better handling of news feed errors, and avoid cases where they could prevent the front page loading
- Fixed the order publication authors are displayed in list items
- Project Dashboard help link
A full list of changes included in this release can be found in the SEEK v1.8.1 release notes
Release data: February 12th 2019
- openBIS integration has been extended and improved upon, mainly through contributions from Tomasz Zielinski of SynthSys. The extensions include linking between Studies and openBIS Experiments, and Assays and openBIS Objects. Automation has also been added to automatically detect and synchronise new items. For more information please read our Guide for using openBIS with SEEK. Note that to use the new features, openBIS 18.06.1 or later is required.
- A new Project Dashboard has been added, to allow project members to view various statistics and trends, including graphs, within their project. For more information please read the Project Dashboard Guide
- Former project members, that have been marked as inactive within a project, are now more clearly indicated along with the date they left.
- Project start and end dates can now be defined for a project, which, if defined, are displayed on the Project page.
A full list of changes included in this release can be found in the SEEK v1.8.0 release notes
Release date: November 19th 2018
- Fix to a bug where the session table column was too small. This sometimes led to a datafile upload problem if the user was in a large number of projects.
- Show the Project creation date on its show page. (In 1.8 we plan to include the option to specify the project start and end dates).
- Fix to a bug where some assets couldn’t be edited if shared across multiple projects, and the user only belonged to a subset of those projects.
A full list of changes included in this release can be found in the SEEK v1.7.1 release notes
Release date: October 15th 2018
- Programme wide sharing permissions have been added. The sharing options now include the ability to share across a whole Programme.
- ISA graph improvements - we spent some time revisiting the ISA graph, fixing some underlying issues and making it more usable. It now defaults to showing the tree view, and the graphical view is simplified and highlights the current item and its nearest neighbours. It no longer includes the associated Project and Programmes to avoid unnecessary interlinking and complexity. The intention is that the graph view should provide a quick visual indication of the place of the current item within the ISA network, and provide the ability to explore and navigate over the graph. A separate export function has been provided to all easy generation and download of PNG files for inclusion in reports or presentations.
- A dedicated NCBI ID sample attribute type has been added, which accepts a number and displays as an identifier URI. If the NCBI id matches an Organism present in SEEK then the link will automatically be made.
- Restrictions to Sample Type visibility have been added. Sample types are now initially only visible to members of the Project they are associated with, until it starts having Samples associated with it. The Sample Type will become visible outside of the project, and to external users, once one or more samples associated with that Sample type have been made public. This allows more freedom to allow all project members to create Sample Types, without the difficulties of having full sharing permissions on Sample types, whilst restricting the Sample Types exposed outside of the Project.
- The ability to link Documents to Events, and vice versa, has been added.
A full list of changes included in this release can be found in the SEEK v1.7.0 release notes
Release date: August 21st 2018
- Fix to prevent users flagged as having left a project being able to access items shared with that project (they can still access their own items, or items also shared within them in other ways)
- Fix to an error occuring when a large number of Documents are associated with an Assay
- Fix to manually adding an organism manually through its NCBI ID, when the ID URL is provided with surrounding spaces.
A full list of changes included in this release can be found in the SEEK v1.6.3 release notes.
Release date: July 5th 2018
- Fixed a bug when viewing a Project page that has more that 5 visible Documents associated with it.
- Avoid warning about missing projects when uploading a standard Excel file, being mistaken as RightField template.
- When running SEEK through Docker, write the Puma output and error logs to files.
A full list of changes included in this release can be found in the SEEK v1.6.2 release notes.
Release date: June 20th 2018
Bugfixes and some small improvements, in particular
- Fixed an error when uploading a DataFile with no Assays in the database (only seemed to affect Docker)
- Fixed a mime type problem when uploading files, in particular CSV files being incorrectly treated as Excel
- When using the DataFile upload wizard, the arrow keys no longer affect navigation whilst editing a field
- Recognise and handle Excel (macro-enabled), XLSM, files as standard Excel files.
- Within the admin area, when showing the queued jobs, there is no a button to clear failed jobs.
- You no longer have to accept the (blank) Terms and Conditions when setting up the first user for a new SEEK installation.
There have also been a few other smaller fixes and improvements, a full list of changes included in this release can be found in the SEEK v1.6.1 release notes.
Release date: June 8th 2018
Major changes include:
- Interlinking the ELIXIR Norwegian e-Infrastructure for Life Sciences (NeLS) with the SEEK platform. This will provide NeLS and SEEK users with unprecedented opportunities for storing, sharing, and archiving of data in ways that comply with the FAIR principles.
- Our second installment of our JSON API, in particular to include support for writing and submitting new entries in SEEK. Most write abilities are now available through the API including creating Datafiles, SOPs, Models, Investigation, Studies and Assays and linking them together. More details about the api can be found in the API Guide, with more technical details found in the JSON API Overview
- Changes to the DataFiles upload workflow, along with better RightField template support. The flow has been changed such that the file is registered before providing additional details. This allows information to be extracted and details automatically populated where possible. The supported templates are now provided as part of the templates generated for Sample Types, but will soon be available more widely.
- DataFile metadata is now provided through a Wizard, split into logical steps, that can easily be stepped through.
- Assays can be created and linked to the DataFile being submitted as part of the same process. This can either be manual or from the details provided within a template.
- Support for a new Document asset type. This is to represent general documents that do not fit as other asset types - such as reports or meeting minutes.
- Ability to enable and provide Terms and Conditions, that need to be accepted as part of the registration process
- Creating DOI’s for individual items has been made clearer and easier to use.
There have also been many other bug fixes and small improvements. A full list of changes included in this release can be found in the SEEK v1.6.0 release notes.
Release date: February 20th 2018
Bugfix release that includes:
- Minor security fixes, following an external security review (more details available later)
- Image scaling fix - where some avatars were scaled down, and then expanded causing them to appear blurred.
A full list of changes included in this release can be found in the SEEK v1.5.2 release notes.
Release date: January 11th 2018
Bugfix patch release that in particular fixes:
- An error that prevented people entries being deleted in some cases.
- An error turning exception emails on or off in the admin settings
- An error that prevented a Programme submission being rejected
A full list of changes included in this release can be found in the SEEK v1.5.1 release notes.
Release date: December 11th 2017
This is quite a large release, and the main highlights include:
- Our first released version of our JSON API. This has been built to conform to the JSON API specification, and is documented on SwaggerHub. This read API has been developed in conjuction with, and feeds into, a write API which will be released incrementally in subsequent releases. For more details please read API.
- Incorporating the new JERM 2 ontology, along with updates and extensions to the RDF produced by SEEK.
- Migrated legacy sharing permissions: Given registration for SEEK is open to anyone, we have removed the ability to administer sharing permissions of items for “all registered users”. This ability was removed from the user interface several versions ago, but a number of items retained this legacy sharing permission. Items shared with “all registered users” have now been updated so that their sharing permission is “project wide” instead, according to the projects the item is associated with. This restricts the audience which can interact with the item. Owners and managers of items are still free to continue to choose and change the sharing permissions as they wish.
- If users wish to request to join a project, but do not know the user that administers it, there is now a button available to do so. A message will be sent the administrators of those projects with additional details. When added to a project, the new member is automatically notified by email. A request can only be sent once every 12 hours.
- DOI’s and ORCiD identifiers, where used or created, are now displayed more clearly in various views and lists.
A full list of changes included in this release can be found in the SEEK v1.5.0 release notes.
Release date: September 4th 2017
Contains bug fixes and minor improvements, and also in particular a reorganisation and update of the Administration areas of SEEK.
A full list of changes included in this release can be found in the SEEK v1.4.1 release notes.
Release date: July 4th 2017
The main change in this version is a complete upgrade of the underlying platform to the Rails 4.2, which supports Ruby 2.2.
Other major changes are included below:
- Upgrade to Rails 4 platform
- Project sharing permission defaults for when adding new items for a Project.
- Events are included in the ISA graph, and the text formatting has been improved
- More descriptive tab titles
There have also been many bug fixes (although many of the bugs listed in the release notes relate to problems encountered during the Rails upgrade)
(A future upgrade to Rails 5 is planned for the future once that version has stabalised and our dependencies have been updated)
A full list of changes included in this release can be found in the SEEK v1.4.0 release notes.
Version 1.2.3, 1.3.3
Release date: June 23rd 2017
Patch release to fix an issue, where items shared with “all registered users” in older versions of SEEK may be shown publicly.
Release date: May 10th 2017
Patch release that fixes some bugs, in particular:
- Fixes an issue to do with editing sample types after a validation error
- Fix to displaying samples or sample types linked to a large number of projects or other associated items
- Clarifies publication authors when the person that registers it is not an actual author
- Fix for when using older version of Sqlite3
A full list of changes included in this release can be found in the SEEK v1.3.2 release notes.
Release date: April 27th 2017
Patch release that fixes a few small bugs, in particular:
- Fix to sharing form for Studies and Assays
- Fix searching error where a spreadsheet was incorrectly expected
- Fix selection of default license for a project
- Fixes related to strains and extracting sample strains
A full list of changes included in this release can be found in the SEEK v1.3.1 release notes.
Release date: March 17th 2017
This is the first public release that supports openBIS integration. This version includes
- Ability to link and browse an openBIS space and datastore, and browse DataSets
- Easily register an openBIS DataSet with SEEK as a DataFile
- Browse and download individual DataSet files, or download as a whole zip file.
- Search indexing of registered openBIS DataSets
- Automatic synchronisation with openBIS spaces and DataSets
- An openSEEK bundle that provides both SEEK and openBIS through Docker and Docker Compose.
- A new UI for setting sharing permissions
- Now displays a matrix for easier setting and viewing of individual permissions, replacing the pre-canned options that weren’t always that intuitive or logical.
Details on how to use openBIS with SEEK is available in our User Guide
A full list of changes included in this release can be found in the SEEK v1.3.0 release notes.
Release date: March 3rd 2017
Fixes a couple of issues caused by some missing CSS (Stylesheet) elements related to Samples. Although minor this affected some of the functional behaviour.
A full list of changes included in this release can be found in the SEEK v1.2.2 release notes.
Release date: February 21st 2017
Small bug fix release to fix:
- Crossref endpoint for DOI querying requires https://
- Better DOI and Pubmed validation
- Manual entry of publications currently disabled
- Further improvements to authorization caching update speed and fix a small inconsistency with incomplete user registrations
A full list of changes included in this release can be found in the SEEK v1.2.1 release notes.
Release date: January 23rd 2017
Large update with many new features and improvements, in particular a new approach to handling Sample information.
- A major reimplementation and design of our support for Samples
- Developed as part of our discussions within the FAIRDOM-ELIXIR Samples Club, which was setup specifically to overcome problems with our old BioSamples
- Flexible system that allows users to design their own Sample Type standards, which are associated with an
extractable spreadsheet template
- Templates can be autogenerated, or Sample Types created from existing templates.
- Sample Types contain a user designed set of attributes, and attribute types. Validation is included to check a value matches its type, or if specified as ‘required’ a presence check is carried out.
- Units can be optionally associated with a Sample Type attribute.
- Sample Types can be interlinked, for example a Tissue Sample Type may link to a Patient Sample Type
- Samples can be added to SEEK according to sample type. They can either be added manually, or many can be extracted from an uploaded data file that originated from the associated template.
- An attribute can be linked to a controlled vocabulary which enforces a set of values. This also puts in place future support for CV’s from standard ontologies.
- Assays were updated to now represent the first of many future processes, which can receive and produce sets of samples. UI improvements were made to support easily associating many samples to an assay in at once. A Process describes the changes a Sample may go through.
- This new framework now has possibility to support the SampleTab standard, allowing SEEK to deposit to the EBI Biosamples registry
- A more flexible approach to handling Samples was an important requirement for full openBIS integration.
- It is a framework that can be built upon and enhanced according to user needs in future versions.
- There is documentation available in our SEEK Samples User Guide
- An improved Graphical and interactive ISA graph viewer. It now contains all details but expands as the user interacts with it, avoiding the problem of over-complex graphs. A tree view is also now available to navigate the graph, which includes the Programmes and Projects. A full view of the graph is available if necessary.
- Authorization speedup. A significant improvement in speed and scale when updating the permissions of an item, or a person changing state (e.g. to a new role or project). For performance reasons authorization is cached, which needs updating when a state changes. This resulted in a noticeable delay observed between users when permissions are changed (as a background task updates the cache), sometimes causing confusion. This delay has now been significantly reduced, and the delay is not dependent on the number of items.
- Support for Docker, along with documentation. Docker images are automatically built for
different versions and can be run either as a single container or multiple micro-services split across different containers.
Handles upgrades and persistent data. Docker allows SEEK to be setup and run with a single command. This our expected
approach to simple packaging of SEEK with openBIS.
- Documentation on using SEEK with Docker is available in our Docker Guide
- A Project administrator may now specify the default license for their project which is automatically selected when creating a new item, but can be changed by the user if necessary.
- Improved usability of adding new Publications from a DOI or PubmedID
- Arbitrary URL schemes for remote files, that can be handled outside of SEEK. For example, and scp:// url could be provided for and openSSH based resource
- Storage metrics in one place available to SEEK administrator, split by Project and Programme. Provides a single place to monitor storage rather than checking each Project page.
A full list of changes included in this release can be found in the SEEK v1.2.0 release notes.
Release date: September 30th 2016
Fixes and small improvements, in particular:
- A new My Items page, available from the account menu, which gives quick access to your own items
- Fix to browsing text files, which was a particular problem for CSV and TSV files
- Models simulation page can now be shared as a URL by copying from the browser.
- Fix to include creators of Investigations, Studies and Assays in related items page
Small fixes and minor improvements - for full details see SEEK v1.1.2 release notes
Release date: June 21st 2016
Small fixes and minor improvements - for full details see SEEK v1.1.1 release notes
Release date: June 15th 2016
- New icons and front page changes - in particular
- New and improved SEEK logo - http://goo.gl/NeALVA
- New default avatars for Project and Institution
- New logos for Investigation, Study and Assays
- New logos badges for the different roles
- Support for Programmes to define funding codes
- Licensing of assets. Existing assets will default to ‘No License’. For more information please visit Licenses
- Ability to publish and create Research Object snapshots for Studies and Assays, along with assigning a DOI. Previously only the larger Investigation package was supported
- Display storage usage information for Programmes and Projects, visible to administrators.
A full list of changes included in this release can be found in the SEEK v1.1.0 release notes.
Release date: April 1st 2016
Upgrade fix that avoids a possible error in some cases when upgrading from a fresh 0.23.0 version of SEEK.
Release date: February 9th 2016
Patch release with some minor improvements and bug fixes, in particular
- Corrected the information sent to project administrators when a new person signs up
- Removed some redundant pages
- Fix to application status report page for monitoring
- ORCiD only mandatory during registration, not when creating profiles (if this configuration is turned on)
A full list of changes included in this release can be found in the SEEK v1.0.2 release notes.
Release date: December 15th 2015
Patch release with a couple of bugfixes.
- Fixed the back-button after search
- Prevent email password being auto filled by browser
Also added support to start easily and safely adding links to help pages in user guide.
A full list of changes included in this release can be found in the SEEK v1.0.1 release notes.
Release date: December 8th 2015
Self management of Programmes and Projects
- Standard users can create their own Programmes.
- This feature can be turned off by a SEEK administrator if not required.
- An administrator is required to approve the created Programme.
- The creator of Programme can administer it, or allow somebody else to administer it.
- A programme administrator can create Organisms.
- Improvement to roles
- Project manager becomes Project administrator.
- Asset manager becomes Asset Housekeeper - and can now only manage assets for those who have been flagged as leaving a project.
- Gatekeeper now becomes Asset Gatekeeper.
- Introduced Programme administrator, who can create and projects and become their administrator or assign somebody else as an administrator.
- Roles will be fully documented in more detail in the near future.
- A project administrator can flag somebody as having left a project.
- Better and easier management of project members and roles.
Investigation Snapshots and publication
- Support for creating a Research Object for an Investigation to form a Snapshot.
- This allows an Investigation to be frozen in time for publication, whilst allowing it to continue to change in the future.
- Support for easily and quickly making a full Investigation publically available.
- A DOI can be generated and associated with an Investigation Snapshot.
- If configured, a snapshot can easily be pushed to Zenodo.
Improved support for remote and large content
- Presentations added as Slide share or Youtube links will now be rendered within SEEK.
- This introduces a rendering framework that makes it easier to add new renderers and in the future make it easier for 3rd party developers to contribute renderers.
- Improved handling of remote and of large content.
- Biosample support has been deprecated and disabled.
- Biosamples will be improved and reimplemented as our next major feature change.
- Biosamples can be re-enabled by an administrator.
- If you currently use the Biosamples that was available in SEEK please contact us.
Help pages link
- Help pages can now be hosted externally and an administrator can point to the source of them.
- From past experience, we find it much easier to maintain and update our own Help pages and documentation outside of SEEK, allowing us to expand and improve on them between releases.
- Our documentation will now be published and maintained using GitHub pages making it easier to maintain between versions and receive Contributions.
- Internal help pages are currently still available, but could be deprecated in a future release. If you edit your own internal pages please contact us.
- Improvements to ISA graph rendering.
- Better reporting of the source of error, if an error occurs with a 3rd party service integration.
- ORCiD field can be made mandatory during registration.
- File extensions and urls are indexed for search.
- Imprint/Impressum support.
A full detailed list of changes included in this release can be found in the SEEK v1.0.0 release notes.