Latest version - 1.4.0
Please see Getting SEEK for details about installing SEEK
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.
For previous releases please visit our Earlier Changelogs.