Recent changes

Here is a list of recent changes included with each released version of SEEK.

For details for how to download, install and upgrade SEEK please read Getting SEEK

If you are running your own installation of SEEK, please fill out our Registration Form.

Version 1.0.0 (8th December 2015)

For this version, and future versions are logs have moved to our new SEEK Documentation pages.

Please goto

Version 0.23.0 (6th October 2015)

  • User-interface Re-engineering. This is the most significant change in this release and presents a complete new look to the user-interface. Built upon the popular Bootstrap HTML, CSS and Javascript framework. Alongside adopting the new framework, effort was made to provide an interface which is cleaner, consistent, and simpler.
    Also, adopting the Bootstrap framework makes future development and design decisions quicker, and allows us to more easily support different browsers and mobile devices. Contributing developers can now work with a framework they are either already familiar with or is well documented and supported online, which benefits the long term sustainability of SEEK.
  • Linking Studies and Investigations to publications. Requested by our users an entire study or investigation can now be linked to a publication registered with SEEK. Assays and assets could already be linked to a publication, but sometimes it was necessary to link to multiple items when instead linking higher up the ISA tree is more appropriate.
  • Additional creators for ISA entries. If other people were involved in an assay, study or investigation, they can now be defined directly on the item.
  • Imprint (or Impressum) support. This is legally required in some countries, including Germany. This can be configured by a SEEK admin. For an example see our own imprint on FAIRDOMHub
  • PostgreSQL. Support for the PostgreSQL database has been added and included to our test suite.
  • Update to BiVeS - the model comparison tool - to the latest version

A detailed list of changes, including minor changes and bug-fixes, are available for 0.23.0.

Version 0.22.1 (1st June 2015)

A maintenance version that fixes a number of bugs and provides some improvements.
Details of what has changed and been fixed can be found in the 0.22.1 release notes.

Version 0.22.0 (16th March 2015)

  • Support for DOI's. It is now possible to generate and register a DOI for an asset in SEEK. To do so the item has to be published and visible.
    A DataCite contact is required as you will need the credentials to access the DataCite API. We will be extending this to support DOI's for whole Investigation, Studies or Assays in future releases.
  • JWS Online upgrade. SEEK has been updating to use the new version of JWS Online, with a much improved interface for simulating models.
  • Experimental Faceted Browsing By enabling faceted browsing, you can filter lists of assets or search results. It provides an easy way to explore and navigate through large amounts of items, enabling the items to be accessed and ordered in multiple ways.
  • Ontology term selection and creation. Some projects, like Virtual Liver do not like to write and maintain their own ontologies, and prefer something more lightweight. Therefore we allow the ability for users to define their own extended ontology terms for assay and technology types, outside of the ontology, through the web interface. These terms can be later curated and added to the ontology, and SEEK will automatically synchronise and update to use the terms added from the ontology. RDF that is generated for
    a suggested term uses it's defined parent until it has been added to the ontology being used.
  • Administration improvements. There is a new section for users and administrators management, where an admin can check and perform some actions, e.g. send activation link, delete invalid users or profiles, etc.
    A new application logo can be uploaded directly rather than copying onto the server file system manually. The rebranding options have been simplified, based on our experience that some options are used in the same meaning.
  • Improved ISA Graph. The ISA graph how now been simplified by default, to show a reduced number of nodes for complex and deep ISA structures. It can be toggled between a full and reduced ISA graph.
  • Reduced memory and processing overheads when indexing spreadsheets. The mechanism for indexing has been changed to use OpenOffice, giving a reduced overhead since only the text and not the structure is needed for the search indexing.
  • Improved mime type handling. Improvements have been made to recognising the mime type of files uploaded, for certain browsers.
  • Support for PostGreSQL. PostGreSQL is now fully supported for SEEK, in addition to MySQL and Sqlite3. PostGreSQL is continually tested and will continue to be supported in future releases.
  • A simple status page. Useful for automatic monitoring, a simple page has been created that shows a line of text to show if back ground services are running, seek is up and search is enabled. This page can be found at statistics/application_status, e.g.

A detailed list of changes, including minor changes and bug-fixes, are available for 0.22.0.

Version 0.21.0 (23rd October 2014)

A large part of this version incorporates and synchronises with work done by BioVel on their portal at . This portal is based upon SEEK, but with different configurations. Some work was carried out to provide additional configuration to SEEK to allow both projects to work within the same codebase.

Along with this work we also added

  • Ruby 2.1.3. Although SEEK still supports ruby 1.9.3, we now offically support ruby 2.1, currently 2.1.3. This provides better performance, and allows us to keep SEEK secure.
  • Ontology integrationA configurable ontology is now directly embedded within SEEK, and is read from and used directly. Previously a representation of the ontology was stored in the database. This change now gives us greater freedom to update and change the ontology without the large overhead of having in update the mappings within SEEK. It also now allows other projects to use their own ontology to (start with) describe their experiments.
  • Better control for project managers to administer their projects. In particular adding new users and institutions, and doing so with a better interface for the project as a whole.
  • Programmes.This mostly affects the SysMO SEEK, and allows us to continue to support new projects and users beyond the SysMO funding. Programmes provide an additional umbrella grouping for projects. So, as a real example, the SysMO-SEEK at no longer only supports SysMO, but can now support new programmes of work. SysMO just becomes one of many programmes. We have big plans for programmes in the future, making SEEK more open and available to Systems Biology researchers with programmes they can self-manage and maintain.
  • Fixes and guidelines for running under a sub-uri (i.e. http:///seek) and also running on Fedora.

This is our last version that will be available with Mercurial at BitBucket. We have now moved to GitHub at -

A detailed list of changes, including minor changes and bug-fixes, are available for 0.21.0.

Version 0.20.0 (9th June 2014)

  • Asset pipelining. This is an infrastructure change, that boosts performance and improves caching. It means that all images, including avatars, javascript and stylesheets are optimised and cached by the browser reducing the amount of information retrieved and how often it needs to be fetched.

    This both reduces load on the server running SEEK and reduces the network bandwidth required to interact with SEEK - particularly important at places with poor internet such as conferences.

    If you administer a SEEK site, please pay particular attention in the upgrade notes for the step to compile the assets and how to configure Apache to cache.

  • Direct ontology integration. In previous versions of SEEK, a copy of the JERM ontology was stored within the database. This caused many issues with keeping SEEK synchronised with the ontology changes.

    This has now been replaced by a direct (configurable) link to the ontology file, along with automated synchronisation. Not only does this allow us to more freely and easily update and improve our JERM ontology, but also allows customised installations of SEEK to use their own ontology terms.

  • BiVeS Integration for model comparison. The BiVeS library, developed by Martin Scharm at the University of Rostock, provides the ability to compare differences between versions of an SBML model at the XML level, giving clear indications of what has changed whilst the model has evolved.

    With Martins help, this has been integrated into SEEK to provide comparisons between models.
    We will be providing more information on this in a future blog post.

  • Spreadsheet exploring improvements. Paging and better caching of the spreadsheet exploring has been added, to improve usability and support for large spreadsheets.
  • BioPortal update. The integration with BioPortal has been updated to use their new API.

A detailed list of changes, including minor changes and bug-fixes, are available for 0.20.0.

Version 0.19.1 (15th January 2014)

Along with some performance improvments and bugfixes, this version of SEEK contains a couple of significant improvements in reaction to feedback and user requirements.

  • New Cytoscape graph for the ISA view. We have replaced the navigation of the ISA structure and related items. This gives an improved view where there are many interconnected items, and is clearer about what is connected to the currently viewed items.
  • Roles are explicitly associated with a project.. The roles Asset Manager, Gatekeeper, Project Manager and PAL (and possible future roles) were previously only associated with a person. This caused problems when a person was associated with more than one project. This has now been enhanced so that these roles are assigned to a person in combination with a project, and only come into affect within the context of that project.

As usual a more detailed list of release note changes are available for 0.19.0 and 0.19.1.

Version 0.18.3 (17th October 2013)

A stabalised release of SEEK, containing mostly bug fixes.
It also adds support for ORCID identifers for profiles.

A list of changes are available for 0.18.1 and 0.18.2. The only change to 0.18.3 was a security fix for investigations.

Version 0.18.0 (4th September 2013)

  • Rails and Ruby upgrade. This version includes a particularly significant upgrade in our Rails platform - to the latest Rails 3 version. Along with this change, we upgraded to use Ruby 1.9.3. This allows us to more easily keep up to date with latest Rails improvements, new features and security fixes. It also gives a significant performance and scalability improvements. If you are upgrading you should carefully read our Upgrade notes for this version since it is a little more involved than usual.
  • One click and batch publishing. This provides assistance when publishing assets, either single items or multiple ones in one go. There is a guided process, that suggests and allows the selection of, associated items you may wish to publish together. The final step is a summary of what was published.
  • Improved Tabs. We have improved the top menu tabs, splitting into 2 layers. This will allow us to provide more options and improve the appearance on smaller screens.
  • Customisation. Requested by other projects wanting to adapt SEEK to collect data in other disciplines, we have made some elements of the text customizable (for e.g. Experiment instead of Assay), and also made the storage location of data configurable.
  • RDF Triple Store. We have added a framework for integrating with an RDF Triple or Quad store, which is updated automatically whenever information changes within SEEK. The integration also allows for SPARQL queries from within SEEK itself, which we will be making use of in future updates (such as faceted browsing). Currently we only support Virtuoso, but the framework has been designed to allow other stores to be integrated easily with a small amount of code. Please contact us if you wish to add another triple store of your choice.
    You can find out more about setting up Virtuoso with SEEK in our Guide.

A fine-grained list of the changes can be found in our Release notes

Version 0.17.1 (30th June 2013)

  • Adding initial support for generating RDF, from the data within SEEK and also from RightField enabled templates. This puts in place our RDF generation framework, and supports some key terms from our JERM ontology, and other common vocabularies such as Dublin Core and FOAF. This is still in its initial stage, but now the framework is in place we will be building upon and improving it in future releases.
  • Some performance improvements, in particular for pages that include a wide spread of related items, such as Project or People pages.
  • A new feature to allow discovery of Data files that may be related to a Model, and vice-versa. This currently uses the Sunspot solr engine to search or order according to matching terms. In the future we intend to extend this to take advantage of the RDF and annotations provided by models.

A full list of the changes can be found in our Release notes

Version 0.16.3 (19th April 2013)

A set of small bugfixes, in particular a critical error when adding a resource as a link from a Windows browser.
A full list of the changes can be found in our Release notes

Version 0.16.2 (5th March 2013)

  • Some bugfixes to adding Models files, particularly when adding via a URL, and improvements to how the files are displayed.
  • Fix for when downloading models as a single zip file, previously the zip file could be empty or corrupt.
  • An upgrade to Rails 2.3.17

A full detailed list of changes can be found in our Release notes

Version 0.16.1 (22nd February 2013)

  • Several performance improvements, improving page load time between 2x and 10x depending upon the page and the amount of associated data.
  • Adding a link to a webpage rather than a data resource, is now recording and displayed as a link to another page. This is for linking to external datasets, such as GEO.
  • Bugfixes and UI tweaks

A full detailed list of changes can be found in our Release notes

Version 0.16.0 (22nd January 2013)

This is a large upgrade to SEEK that includes a number of new features:

  • It is now possible to view a variety of Asset documents - PDF, Open Office, Microsoft Powerpoint, Word, and images, text plus many more formats - directly within SEEK in your browser, rather than having to download it first. This requires that you have download privileges for the Asset. You can view the Asset by clicking "View Content" at the top of the page. Spreadsheets continue to be viewed using the Spreadsheet explorer.
  • All the document types that can now be viewed in the browser, as described above, are now processed and indexed to allow them to be discovered by searching in SEEK.
  • It is now possible to register and upload multiple files for a single Model in SEEK. Along with this a separate image can be uploaded along with the Model (such as a schema diagram), which is displayed together with the Model. The files can be downloaded individually, or downloaded together as a zip file. This feature was added with contributions from Virtual Liver.
  • If you wish to share a private item with somebody not registered with SEEK, before making it public, you can now do so by creating a temporary link. This is useful, for example, if you need to share a dataset with a reviewer of a paper, but the paper has not yet been published. The temporary link can be created from the edit page of any asset, and an expiry time can be set - after which the temporary link will no longer work. This feature was added with contributions from Virtual Liver.
  • Based on feedback from our users, we've replaced the drop-down box for creating new assets on the top left, with a more prominent "Create" button. This was due to feedback suggesting that for some users it was not clear on how to add new items.
  • A "My Project" button has been added to the left hand side, to provide speedy navigation to your projects main page.
  • The JWS Online simulator applet embedded into SEEK has been replaced with a Javascript based simulator. This streamlines the integration, and removes some of the security warning related to using applets.
    The simulator itself has been improved over the previous versions, allowing you to browse the schema for reaction, parameters and rate equations. There is still ongoing work to improve the simulator further which will automatically be included in SEEK as it is updated on JWS Online.
  • We've made the Help, FAQ and Template pages more prominent to new users getting started with SEEK. There is now a box on the home page that guides you to these pages, which you can hide once it is no longer
    needed. We have also expanded and updated the guidelines in the Help pages.
  • To improve navigation, and returning to earlier pages whilst browsing SEEK, we've started to add Breadcrumbs to the top of all pages.
  • If there are hidden items within your project that you cannot see there is now an indication, in the list of related items, of the number of items and the person that owns these hidden items. This is so you can contact them to find out more. This is only shown for items related to your a project you are a member of.
  • For those modellers that have files of a format supported by Cytoscape, for example XGMML, we've added additional support for interacting with these files with Cytoscape Web directly within SEEK - allowing you edit the graph which you can then download as a new file. If this feature becomes popular, then we will look into allowing the edited graph to be re-imported directly into SEEK as a new version. This was added as a contribution from Virtual Liver.

There have also been some key improvements to existing features:

  • We've fixed the order that authors are stored and described for publications so that they match the order for the publication. The fix includes retrospectively fixing earlier publications.
  • We've made it easier to link publications to Data and Models directly when adding or updating a publication.
  • As a request from our projects, we've now made a change to the Asset Manager role so that it can now access all assets within their project, including those added as entirely private. This allows the Asset Manager to take control of assets when somebody leaves a project.
  • If an asset is an asset is not linked to anything (e.g an assay or a publication) then the graph view is no longer shown. Previsouly it was shown as a single box, which was being confused with being a download button.
  • We've reduced the header size, at the top of the page, for all but the home page. This provides a little additional space for content without the need to scroll down, especially for users using a lower than average screen resolution.

Of course, there are also many other minor bugfixes and improvements included in this version.

A full detailed list of changes can be found in our Release notes

You can find details about earlier versions of SEEK by visiting our Previous Changes