Monthly Archives: June 2018

Making FAIR data management easier for Norwegian life science researchers.

The new versions of the FAIRDOM/SEEK platform and the ELIXIR Norwegian e-Infrastructure for Life Sciences (NeLS) are now linked. This will provide SEEK and NeLS users with unprecedented opportunities for storing, sharing, and archiving of data in ways that comply with the FAIR principles.

FAIRDOM is committed to ensuring that FAIR data management is simple, practical, and fits in with researchers day-to-day work. As part of this we work with the community in ensuring that key platforms for our partners can integrate smoothly with our data management platforms.

After working closely with our Norwegian Digital Life partners, the new releases of SEEK and NeLS now integrate with each other. This allows access to Norwegian infrastructure for storage, computing and archiving of research data as well as a rich toolbox for FAIR project data management. NeLS supports Norwegian life science researchers in executing Bioinformatics analysis on their data. Using SEEK with NeLS, data or analysis generated within projects can easily be shared among the project participants and made accessible when they are ready for publication.

If you are interested in working with FAIRDOM to integrate with your local or national resources, you can contact us here: community@fair-dom.org

The integration work of NeLS and SEEK has been funded by the Centre for Digital Life Norway and has been performed in collaboration with ELIXIR Norway and FAIRDOM partners at the University of Manchester. Several Digital Life projects have participated in testing of the new versions.

Useful links:

NeLS: https://nels.bioinfo.no/

SEEK: https://fair-dom.org/platform/seek/

DLN: www.digitallifenorway.org

Updates to the FAIRDOM software (SEEK v1.6.0)

A new version of SEEK is now available, and the FAIRDOMHub has been updated with the changes. 

Version 1.6.0

Release date: June 8th 2018

Integration with NeLS

We’ve been working with ELIXIR Norway to facilitate linking of SEEK with the ELIXIR Norwegian e-Infrastructure for Life Sciences (NeLS). This interlinking allows Norwegian life scientists the ability to store and compute Bioinformatics data in the NeLS portal, then link and share this data directly in SEEK. This is a leap forward for Norwegian life scientists in ensuring their data is FAIR.

API

Our JSON API can now support researchers in reading data from SEEK, as well as writing and submitting new entries. This allows all users programmatic access to data published in SEEK, as well as for publishing in SEEK. The current write support covers Datafiles, SOPs, Models, Investigation, Studies and Assays and linking them together. More details about the api can be found in the API Guide. The API will facilitate researchers in embedding SEEK within their day to day data workflows, ensuring better adherance to the FAIR principles.

Data Upload Workflow and Metadata Wizard

We’ve made some changes to the upload workflow that you will encounter when uploading DataFiles, and developed integrated support for templates that have RightField embedded metadata. Now, the dataFile is registered before additional metadata details are asked for. This allows any relevant metadata in the RightField tab of the DataFile to be read, extracted, and used to auto-populate the upload form where possible. The supported templates are now provided as part of the templates generated for Sample Types, but will soon be available more widely.

The Wizard for uploading DataFile metadata has also undergone a revamp, with it now being split into logical steps that can easily be stepped through.

You can find out more details here https://docs.seek4science.org/help/user-guide/templates/master-v1.html

and

here: https://docs.seek4science.org/help/user-guide/data-file-upload-wizard.html

Creating Assays from the DataFile

Ever got stuck when uploading a DataFile and wanting to link it to an Assay, but realising you haven’t created the Assay you want to link it to? Well, now 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.

New Document Asset Type

Have you ever wanted to upload a deliverable, report, meeting minutes or other project management document in SEEK, but not felt there was a suitable asset type? We have now created support for a new Document asset type. This allows you to catalogue general documents that do not fit as other asset types.

Terms and Conditions

When you install and manage your own SEEK, it is important you are also able to provide your users with information about theTerms and Conditions that must be accepted as part of the registration process. This is now configurable by Admin of the SEEK installation. 

Simplified DOI creation

We have simplified the interface for creating DOI’s for individual items. It is now clearer when looking at an individual item how to mint a DOI for that item.

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 Change Log.

Job Posting: Senior Advisor (2.5 yr) in Data Management for the Digital Salmon

Join our Norwegian partners as a Data Manager. Working with colleagues accross Norway, with continued support from the FAIRDOM Team and network. Would suit an early career data manager making their first steps, or a more experienced scientist transitioning into support a role.

Senior Advisor (2.5 yr) in Data Management for the Digital Salmon – Ref.no 18/03082

Required qualifications: PhD or MSc in relevant field of bioinformatics, systems biology, informatics, librarianship, or similar.

The Data Manager will be associated with the project “Towards the Digital Salmon: from a reactive to a pre-emptive research strategy in aquaculture (DigiSal)“. The project is part of the national consortium for biotechnology, Centre for Digital Life Norway, and a partner in the FAIRDOM foundation for scientific data management according to the FAIR principles: Findable, Accessible, Interoperable, Reusable. Main tasks:
Help design the architecture of the Digital Salmon knowledge base, in close interaction with the researchers that will contribute to and benefit from the knowledge base, and with partners that provide technical solutions. Users include bioinformaticians and wet-lab researchers who generate omics data and microscopy images, and systems biologists who develop physiological models e.g. of salmon metabolism.
Be our contact point with the FAIRDOM consortium, benefitting from community support and training in cutting-edge tools and workflows, and contributing to FAIRDOM’s future development.
Be involved on the national level in Digital Life Norway’s development of data and model management.
https://www.jobbnorge.no/en/available-jobs/job/153484/senior-advisor-in-data-management-for-the-digital-salmon-refno-18-03082