Category Archives: Uncategorized

A new version of SEEK is now available, version 1.7.0

A new version of SEEK is now available, version 1.7.0. Full details can
be found at https://docs.seek4science.org/tech/releases/

Highlights include

– Programme wide sharing permissions
Researchers can now apply the fine-grained sharing permissions of assets in SEEK to share with whole programmes. This offers our researchers further support in making data “as open as possible, as closed as necessary”.

– ISA graph improvements
The ISA graph has been modified to provide better visuals for larger ISA structures. In addition we also offer a list-style view of the ISA structure for those wanting to navigate their assets with a more traditional view. You can find screen shots, and further information in our documentation https://docs.seek4science.org/help/user-guide/isa-overview

– Changes to Sample Type visibility
A Sample Type now only become visible outside of a Project if it has public samples associated. This change has allowed us to open up Sample Type creation to all members of projects, where previously only project administrators were able to create sample types.

– Special support for for NCBI sample attribute types
Users can now select NCBI IDs as a special sample attribute. This allows automatic linking with Organisms registered in SEEK. This is part of our ongoing work to replace SEEK strains with a dedicated Sample Type.

– Linking Documents to Events, and vice versa.

There has also been quite a bit of back-end maintenance and tidying up.

The guide to upgrade is available at
https://docs.seek4science.org/tech/upgrading.html. Note that with this
version Ruby 2.4 is required, using 2.2 or 2.3 will result in errors.

The fairdom/seek:1.7 docker image is also available, and upgrading for
Docker Compose can be found at the end of
https://docs.seek4science.org/tech/docker/docker-compose.html

We Are Providing Data Management Support for the Second ERACoBioTech Call.

FAIRDOM currently supports more than half of the projects from the first ERACoBioTech Call in their data management. We are offering our support services for the second  ERA CoBioTech call. We can work with you to draft your data management plan, and then provide software, training, and support throughout your project. We will be holding webinars on the following dates.

Webinar Dates and Times for Second ERACoBioTech Call

Monday 29th October 2018: 13:00 GMT / 14:00 CET
Wednesday 7th November 2018: 14:00 GMT / 15:00 CET
Tuesday 13th November 2018: 11:00 GMT / 12:00 CET

To register, please fill in the google form: Webinar Registration

For more information please visit: https://fair-dom.org/eracobiotech-proposal-support/

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.

Digital Life Norway have written a blog post that goes into some more detail: https://digitallifenorway.org/gb/blog/doing-fair-data-management-is-now-easier-for-norwegian-life-science-researchers

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.

Join us at “FAIR Data Management in Life-Sciences” a workshop and user meeting in Lyon France, Sat 27th Oct.

We are hosting a workshop and user meeting entitled “FAIR Data Management in Life-Sciences”, as a satellite of this year’s ICSB 2018, in Lyon, France (http://www.icsb2018-france.com/). To register, please fill in the google form below (or follow this link directly to the form http://bit.ly/fairdom-workshop), which also provides some additional information about the workshop and user meeting. If you can not view the google form, or do not wish to register your details using a google form, please mail community@fair-dom.org and one of the team will collect your registration data via email or phone.

Merry Christmas from the FAIRDOM Team.

It has been another fantastic year here at FAIRDOM.

– We made 4 major releases of our SEEK software, which powers the FAIRDOMHub, bringing you the following functionality:

  1. (v1.2) Added in the new Samples framework, which offers you a more flexible way of managing your Samples, and their associated metadata.
  2. (v1.3) Fully integrated our two flagship platforms SEEK and openBIS so you can now use SEEK to find and link the data and metadata from your raw and processed data stored in openBIS. 
  3. (v1.4) Upgraded to RAILS 4 to ensure the security of the platform, and your data. 
  4. (v1.5) Brought you access to the JSON read API, so you can search for your data programatically. We also released the JERM 2 ontology.

– We attended 16 different community conferences, engaging more than 4000 of you, to help demystify data management, and make sure your valuable data is given the longevity it deserves.
– We attended and facilitated 14 community engagement meetings on your behalf, ensuring that data management policies for the future ensure the best long-term outcomes for your data and the research fields.
– We partnered with ELIXIR Norway, providing SEEK/FAIRDOMHub as an official data management platform for the Digital Life Norway projects. We also provided bespoke integration with NeLS – a data store and compute – which improves the data management pipeline for all Norwegian life-science researchers.
– Provided more than 200 new users with space to manage their data on the FAIRDOMHub, taking us to nearly 1000 users.
– Our SEEK platform was integrated locally into 7 new large scale labs, providing a secure store for their data.
– Held international training events for data management in the UK, Germany, and Norway to ensure researchers had access to hands-on data management training tailored to their work.

Thank you all for your support this year. We have lots of exciting plans for 2018, and we hope to see many of you along the way.

The FAIRDOM Team.

Our final webinars of 2017

We recorded our last two webinars for you all to enjoy over the summer.

You can access Björn Grüning’s talk “Conda and Containers for a sustainable bioinformatic infrastructure” here:

https://fair-dom.org/knowledgehub/webinars-2/bjorn-gruning/

and You can access Matthew Pocock’s talk “ShortBOL: A shorthand for synthetic biology design” here:

https://fair-dom.org/knowledgehub/webinars-2/matthew-pocock/

Digital Life Workshop, Bergen, Norway, 8th May

At the start of this week Natalie Stanford, Olga Krebs, and Ron Henkel, from the FAIRDOM Team, were in Norway providing basic and advanced training for Digital Life Norway.

The agenda for the day included an introduction to FAIRDOM as a whole, followed by a short introduction to Rightfield, then parallel sessions for basic and advanced FAIRDOMHub training. The training goals for the day were:

Basic Training

  • What is the ISA structure?
  • How to create and interlink ISA elements
  • Browsing and downloading information/data from FAIRDOMHub
  • Uploading/registering your own assets in FAIRDOMHub
  • Linking assets to the ISA
  • Registering publications and linking to other assets.

Advanced Training

  • Model management in FAIRDOMHub
    • Creating modelling assay
    • Reproducing modelling experiments registered in FAIRDOMHub
    • Creating SED-ML
    • Creating COMBINE archives
    • Archiving your own modelling work
    • Tracking model evolution
  • Publishing using FAIRDOMHub
    • Why is traditional supplementary data is not enough?
    • What is the ISA structure?
    • Setting up a full ISA structure with attached data and models
    • Making the ISA structure publicly available
    • Snapshotting the ISA and associated data and models
    • Assigning DOIs for linking to within publications.
  • Samples in FAIRDOMHub
    • Learning about the new samples framework
    • Using existing Sample Types within the FAIRDOMHub
    • Using Metadata sheets to describe samples
    • Generating your own samples using forms and templates in FAIRDOMHub

 

 

The workshop was a great success, and the tutorials were popular with all 20 participants. It was particularly rewarding to see how well everyone was working together to learn and solve the data management issues of our example data management conundrum at Happy Salmon Co.

The researchers attending the workshop provided feedback on the technical implementation of both modelling and samples handling in the FAIRDOMHub. As a result we hope to start some user experience improvements over the coming months.

We were well looked after by our Norwegian hosts, and all of us look forward to working more with the Digital Life Norway.

FAIRDOM passes 30 month funding review

On the 27th and 28th March, the FAIRDOM team met in the historic town of Heidelberg in Germany for our 30 month funding review.  The meeting was attended by the whole FAIRDOM team, reviewers, funders, and special guest users Jon Olav Vik from the Digital Salmon project, and Ursula Klingmüller, from the IMOMESIC project.

Over the two days we presented out successes from the last two years which include:

  • Developing our software to allow the users from anywhere in the world join the FAIRDOMHub and self-manage their projects.
  • Establishing the new samples framework, allowing users to define their own templates.
  • Integration of back-end and front-end data management software.
  • Doubling our users of the FAIRDOM platform in the last 12 months, during an exponential growth trend which we expect to continue.
  • Holding our first user meeting, showcasing some of superstar users including Digital Salmon, Siberian SEEK, ERASysAPP, and LiSym.
  • Establishing the FAIRDOM Association.
  • Updated on general support and special project support (e.g. ERASysAPP, Digital Life).

We also had extensive discussion with the funders and reviewers over ensuring sustainability of the FAIRDOM platform and services. The review was a great success and we passed, with a recommendation to release the next two years of our project funding. This is great news for our project, and great news for the growing community of users like you. We will be able to improve and grow our engagement and support over the next few years. We look forward to having you with us on this journey.