Here is a list of recent changes included with each new SEEK version.
Version: 0.9.0 (released 3rd September 2010)
There follows an overview of the main changes in this version, and a detailed list of changes can be found in our Release notes.
Interactive graphical view of I.S.A elements
We have added a graphical representation of Investigations, Studies and Assays, that is interactive and click-able. This is aimed to provide easier navigation and a visual overview of the structure of these elements. We particularly encourage feedback on this feature as it is new and open to further possibilities if it proves useful.
Views over Investigations and Studies are centred on the study. Tooltips provide the full title and type by hovering the mouse pointer over the element. The current element is highlighted with a coloured border.
Views over Assays are centred on the Assay, and includes the Assets linked to that Assay.
Visual indication of asset visibility
Until now, the only way to review the visibility of an asset was to view the sharing policy edit form. To make it easier to quickly see the status of an Asset, we've now added a little icon to the list items that gives a simple overview of the visibility of that item.
Asset authorization performance and maintenance improvements
Recently there was unexpectedly a sudden increase in the volume of data registered with SEEK. This lead to some performance issues when authorizing collections of these assets. Along with this some of the source-code was becoming cumbersome and difficult to understand for unfamiliar developers. For these reasons the authorization modules and underlying data model was refined and significantly improved.
Read-only REST-API
A readable REST (Representational State Transfer) API has been requested for some time to allow third party application to embed SEEK content. This allows SEEK to be wrapped within a dedicated content-management system or wiki, avoiding the need to reproduce existing technology within SEEK itself.
Also important, to support new and existing projects that wish to install a local version of SEEK as their main data management system, this API is useful for automatic registration of content within the main central SEEK instance using a dedicated JERM Harvester.
This API has been developed with Linked Data in mind, and is backed with a comprehensive XSD schema.
There are some finishing touches and minor extensions required, after which we will be publishing documentation and the XSD schema.
Spreadsheet meta-data extraction tooling
To complement RightField, as well as existing spreadsheet templates, we have been developing a simple spreadsheet extraction toolkit. We are now starting to integrate this as part of the REST API. Although not immediately apparent to our users, this is important for future plans for JERM Extraction and richer meta-data and search.
This work is ongoing, and currently provides an XML representation of the contents of an Excel spreadsheet. We expect to extend this to support CSV representation along with support for Open Office spreadsheets.
Administration improvements
Up until recently, SEEK has been maintained and administered solely by the SysMO-DB team. However, recently and in the future we are receiving increasing interest from other projects. This meant that we needed to make the setting up of new instances of SEEK, and administering existing instances, more usable and intuitive.
Version: 0.8.2/0.8.1 (released 6th July 2010)
A small patch to fix a couple of issues. These include better handling of large lists of items, being able to more easily credit members of your project, and allowing PALs to edit ISA elements related to their project.
A full detailed list of changes can be found in our Release notes.
Version: 0.8.0 (released 1st June 2010)
This version includes some significant new features. These both visible improvements within the interface, and back-end changes to may not be immediately apparent.
A full detailed list of changes can be found in our Release notes.
Data storage
The most important back-end change is a change to how we store data. This is now stored and a more efficient and flexible way, which has the most notable improvement of removing a threshold on the maximum upload size for data. However, in our live system it has been configured to impose an artificial threshold of 2Gb, which should be plenty.
An additional change this provides is that it make the downloading of data more efficient and less reliant on the memory capicity of the running server.
Forums
We have also now included a Forums system, including attachments, to allow our users to share knowledge with each other, including specifically Templates and links to external sources. The forums also now allows our users to suggest new features and improvements.
Particularly interesting or useful information that arise through the Forums will by migrated across to our Integrated Help System (see below).
Announcements and Notifications
We've incorporated an announcement and notification system. This allows us to make two types of announcement. There can be announcements that are only listed on the website - items such as new upcoming events and other interesting news items. Also we can make announcements that are emailed to all our users - such as new site releases, or scheduled downtime. Email announcements have an opt-out ability which can be selected by users that no longer wish to receive future announcements (you possibly arrived here through one of these announcements).
Integrated Help system.
We've added an integrated help system. This serves two purposes - the obvious one is to simply better inform our users how to use SysMO SEEK, but the other purpose is as a mechanism for disseminating information such as Data Templates, Controlled vocabularies and external resources.
Other small changes
Along with a number of Bug fixes, we've added some small tweaks and improvements.
In particular: we've allowed Assets (Data, Models and SOPs) to be credited to people not already registered with SysMO SEEK and improved how the content type of an asset is displayed (such as PDF or ZIP file).
We've also made SysMO-SEEK much easier to setup and maintain.
Version: 0.7.0 (released 27th April 2010)
The highlights of this version are the new assay class of Modelling Anaylsis, defining Strains for an Organism, and registrating Publications through either a PubMED ID, or DOI. We have also included an integration with BioPortal, which provides us to define and extend entities within SysMO-SEEK with Ontological terms. This allows us to formally define our controlled vocabularies and the relationships between them.
As always, this release also includes a number of bugfixes, and general improvements.
A full detailed list of changes can be found in our Release notes.
Registering Publications
You can now register a publication if it has a PubMED ID, or a DOI. To register a publication you supply the ID, click 'Fetch', and details about the document are retrieved via a web-service. PubMED automatically provides an abstract, but for publication identified by a DOI you need to provide your own.
Once registered there is then a step to select the authors. If the authors can be found within the SysMO-SEEK Yellow Pages, they will be automatically selected - however if there is a problem selecting the author due to an ambiguity or mis-spelling, the submitter can manually select the appropriate author from a list.
Modelling Analysis Assay
Along with assays for Experimental work, you can new define an assay for a Modelling analysis.
This extends the standard assay to allow you to select a Model, and define Data that has been used, or generated, as part of that Modelling Analysis. The relationships currently defined are "Constuction Data", "Validation Data" or "Simulation Results" - we can extends these relationships if requested.
Defining Strains
When selecting an Organism for an assay, you may now also define the Strain if required. We've pre-populated the database with some Strains we expect to be relevant, but you can also define your own by supplying the appropriate Strain text.
Version: 0.6.3 (released 25th March 2010)
This is a small intermediate release that includes some minor improvements and bugfixes.
A full detailed list of changes can be found in our Release notes.
Version: 0.6.2 (released 17th March 2010)
This is a small intermediate release that includes some minor improvements and bugfixes.
A full detailed list of changes can be found in our Release notes.
Version: 0.6.1 (released 13 March 2010)
This is a small intermediate release that includes some minor improvements and bugfixes.
A full detailed list of changes can be found in our Release notes.
Version: 0.6.0 (released 19th February 2010)
This version finalises the changes required for the first version of what we call the JERM harvesters. These integrate with individual project data management systems, and import Data, SOPs and Models from these sites and register these assets with the SEEK system.
Along with the JERM harvesters there have also been some new features and user interface improvments that are more visible to our users, which are outlined as follows. These are either side effects of the JERM, or improvements requested by our users.
A full detailed list of changes can be found in our Release notes.
Defining asset creators
The uploader of an Asset will not always necessarily be the creator or author of that item. This is particularly true where the asset has been registered via the JERM. Therefore, there is now the ability to define one or more creators for an asset.
Extending bookmarked favourites to all assets
The bookmarking of favourite items has now been extended beyond the Yellow Pages to include all Assets, and also investigation, studies and assays. To bookmark an item, drag its icon to the favourites panel; to remove a bookmark drag it from the panel to the main view.
Bookmarking searches
As with individual items, searches can now be stored as a bookmark to repeat a query in the future.
Listing all and latest items
The alphabetical pagination has now been extended from the Yellow Pages to all views. Based upon feedback we have now also included listing only recently changed items, and a full list of all items.
Version: 0.5.1 (released 5th Febuary 2010)
This is an interim release, and includes a lot of back-end work required to support JERM. JERM is not yet activated in this release, but contains multiple bug fixes and user-interface improvements requested by our users.
A detailed list of changes can be found in our Release notes.
Version: 0.5.0 (released 26th October 2009)
The focus for this release was to include Versioning for all Assets (DataFiles, SOPs and Models) - this was an essential requirement to support JERM integration.
Along with these changes there have also been some minor modifications and bug-fixes. A detailed list can be found in the Release notes.
Below are listed some of the key changes.
Versioning
A new version of a SOP, Model or DataFile can now be uploaded - if you have permissions to edit that asset. A new version is only created if you upload a new file - changing descriptions does not create a new version - however once a new version has been created, previous versions will retain their current descriptions.
To create a new version, and if you have permission, then you can click the "Upload new version" link at the top of the page. This reveals some fields that allow you to select the new file for upload, and also optionally provide some additional revision comments, which we encourage you to do.
Once there are at least 2 versions of an asset, you can view alternative versions and view the revision comments using the control box below the asset title.
Assays are now linked directly to a particular version of a SOP or DataFile. Sharing settings (i.e. who can view and download the file) apply to all versions of an asset, and we will be looking at making this configurable per version in the near future.
Deleting Investigations, Studies and Assays
There was some confusion about when an Investigation, Study or Assay can be deleted. We've now made this clearer by showing a disabled delete button, with an explanation of why you can't delete the item when you otherwise may have been expected to. Investigations cannot be deleted if they have associated Studies, Studies cannot be deleted if the have associated Assay, and Assays cannot be deleted if a SOP or peice of Data is associated with it.
Alphabetical pagination
People,Projects and Insitutions - i.e elements within the Yellow Pages, are now paged alphabetically. This should reduce the size of some of the lists, and also make it easier to find a certain peice of information.
We will be looking at extending this pagination to other lists within SEEK.
Easier Assay SOP and Data file selection
SOPs and Data files are now only listed for your project(s) when constucting an Assay. This was to reduce the increasingly growing list. If you wish to view and select an item from another project, you can opt to do so - in which case all SOPs or Data files, which you are authorized to see, are included in alphabetical order.
Culture growth
Previously Culture Growth was one of many technology types,
but feedback we received indicated that this attribute was so common to all assays that we have seperated it and allowed it to be defined independently.
PALs can add and edit Model types and formats
Pals now have administrative rights to edit and create new Model types and formats. Every project has at least 1 PAL - if you are not sure who the PAL is for your project, look at the people under your project with the 
logo below their personal picture.
Feedback.
This was actually included in the previous version to be released, but was not formally announced. At the top left of any page there is now a link to provide feedback - either feature requests, bug reports or any feedback you feel you would like to report to the Sysmo-DB team. Its possible to send feedback anonymously if you are shy!
We strongly encourage you to provide feedback, as this is how we can improve SysMO SEEK.
