Author Archives: Stuart Owen

FAIRDOM-SEEK 1.11.1 released

A small update for FAIRDOM-SEEK, version 1.11.1, has been released.

This contains contains some improvements and bugfixes, including:

  • Fix to a rarely encountered bug that caused a user to be added to a project with a nil Institution, which could then lead to other problems
  • Fix to remove some warning messages about a duplicate definition of include_blank
  • Person responsible for Study has been deprecated and removed from the user interface

Details on installing FAIRDOM-SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

FAIRDOM-SEEK version 1.11.0 released

We are pleased to announce a new version of FAIRDOM-SEEK is now available, which is version 1.11.0

There have many improvements and bugfixes, but the main highlights include:

  • Changes to joining a project during registration.
  • Simplified Project and Programme creation.
  • Site managed Programmes.
  • Markdown formatting of descriptions.
  • Ontology based controlled vocabularies.
  • Spreadsheet view for exploring Comma and Tab separated value files (CSV or TSV).
  • Condensed view of lists.
  • Table view of lists.
  • MIAPPE support with custom metadata extensions.
  • Bulk changing of sharing permissions.
  • Simplified deleting of Projects.
  • Run with Copasi button.
  • Changing visibility of item versions.

More details about the changes can be found in the 1.11.0 Release Notes.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

SEEK version 1.10.2 released

A new version of the FAIRDOM SEEK software has been made available, version 1.10.2, which includes a few bug fixes since the last release last month.

In particular, it fixes a validation problem with linking to Publications that were added before describing Publication types were available, and do not have a specific type defined.

More details about the changes can be found in the 1.10.2 Release Notes.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

RightField version 0.26 available

A new version of the RightField software has been released, version 0.26.

This version includes the following enhancements

Ability to select invididual terms that will appear within the dropdown list. The previous behaviour forced all subclasses or instances. From the list of terms at the bottom right, multiple terms can be selected by holding down CTRL, or SHIFT to select a range. By default all are selected. Many thanks to Andreas Weidemann for this contribution.

Tooltips are shown to display the term URI when browsing the ontology or selecting terms – this is to help resolves ambiguities.

Increased the default JVM to 1Gb, and increased the timeout limit when loading ontologies. This provides support for larger ontologies.
Please bear in mind, that for some ontologies you may need to be patient for them to load. For example the EFO ontology can take 2-3 minutes on my laptop.

An upgrade of all dependencies, and Apache POI in particular.

The new version can be downloaded from https://rightfield.org.uk/download.html

For some details and background regarding running on Mac OS X please see the Release Forum Post

SEEK version 1.10.1 released

We are pleased to announce a new version of FAIRDOM SEEK is now available, which is version 1.10.1

This minor release contains some bugfixes and small improvements, including:

  • Rails upgrade to the latest Rails 5 release (5.2.4.3), 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

More details about the changes can be found in the 1.10.1 Release Notes.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

SEEK version 1.10.0 released

We are pleased to announce a new version of FAIRDOM SEEK is now available, which is version 1.10.0

There have many minor improvements and bugfixes, but the main highlights include:

  • Filtered search and browsing
  • Enhanced support for publications
  • Adding one or more Discussion Channel links to all Assets
  • 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
  • Renaming of contributor to submitter – to be clearer about what this attribute represents

More details about the changes can be found in the 1.10.0 Release Notes.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

SEEK version 1.9.1 released

We are pleased to announce a new version of FAIRDOM SEEK is now available, which is version 1.9.1

Along with a number of bug fixes this version includes

  • 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 actions between 2 separate pages, rather than being handled together 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.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

Rightfield 0.24 released

A new version of Rightfield, has been released and is now available for download.

The new version includes a refresh and update of all its dependencies, in particular updated to use the latest version of Apache POI.

Along with an update there have also been a couple of improvements:

  • Rightfield will now retain existing data validations, that had been added to an existing Excel document previous to being populated with Rightfield.
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  • Fix to an ambiguity problem with mixed ontologies containing terms with the same label, but from different sources. The ontology hierarchy and term view how includes the namespace prefix where available, and a tooltip will show the full IRI when hovering over a term.

The new version is available to download from the Rightfield website

SEEK version 1.9.0 released

The FAIRDOM team are pleased to announce a new version of SEEK – version 1.9.0

The highlights of this version includes:

  • Major upgrade of the underlying platform
    • Rails 4.2 → Rails 5.2
    • Updating and replacing affected libraries and dependencies
    • Unifying javascript to use jQuery framework throughout, and removing Prototype references
  • 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)
  • A lot of bugfixes and minor improvements discovered during the upgrade testing

The main bulk of this work was the upgrade to Ruby on Rails, the underlying platform SEEK is built upon, which included many changes. This work has been carried out in parallel to other work over several months, and undergone a lot of testing. Bringing things up to date ensures we continue to get feature enhancements, improvements and security fixes.

Details on installing SEEK can be found in our Documentation, at https://docs.seek4science.org/get-seek.html – including running with Docker.

The upgrade guide can be found in the usual place at https://docs.seek4science.org/tech/upgrading.html

New to FAIRDOMHub – Create your own Programmes and Projects

Following the recent release and upgrade of FAIRDOMHub to SEEK version 1.0, we are pleased to announce that we now support creating and administering your own Programmes and Projects.

This means as a registered user you can create your own Programmes, and create and add your own Projects and Profiles and administer them. After creation the Programme will need to be approved by FAIRDOM, but afterwards it can be completely self-managed.

You can register with FAIRDOMHub at https://fairdomhub.org/signup if you do not already have an account.

Please visit our user guide for more details about this new service: http://docs.seek4science.org/help/user-guide/programme-creation-and-management.html

Once you have created a Programme, you will automatically become the Programme administrator. For more information about what you can then do, please read: http://docs.seek4science.org/help/user-guide/roles.html#programme-administrator

If you require any assistance or guidance, please see if your query has already been answered at our Biostar message board at: http://biostar.fair-dom.org/ . If it hasn’t please raise a new question.