Author Archives: community

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.

Katy Wolstencroft shares insights on why data integration is so important.

This month, Katy Wolstencroft from the FAIRDOM team gave an interview to Phys.org. In the interview she talks about why data integration is so important for modern science, and how to go about managing data to make it easier to integrate.

You can read the full interview here https://phys.org/news/2017-10-integrating-data-to-learn-more.html 

If you want to know more about why data management is important, and how to implement in your laboratory, we have starter page you can visit https://fair-dom.org/knowledgehub/data-and-model-management/

FAIRDOM hosting training as part of Synthetic Biology UK in Manchester on Wednesday 29th November.

We are excited to announce our 2017 SynBio Data Management Training Day. The event is co-located with Synthetic Biology UK, in Manchester. The venue will be the Manchester Institute for Biotechnology (http://www.mib.ac.uk/contact/).

The day will run on Wednesday 29th November, from 9.30 to 4pm, you can view the full agenda here https://docs.google.com/document/d/1TMmM7xBPNYGkxJnM1Sst40XjCgBl2bA8X-NdHlnCel8/edit?usp=sharing

During the event we will be showcasing the data management in current UK Synthetic Biology Centres, and offering data management training in SEEK, the official data catalogue used by Manchester and Edinburgh. You can find out more about the event, including the location here https://www.fairdomhub.org/events/99

Participation is free. We have limited spaces, and spaces will be allocated on a first come, first serve basis.

To sign-up, or if you have further questions,  please email community@fair-dom.org

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/

FAIRDOM can support the data management of your ERACoBioTech Bids.

FAIRDOM can support the data management component of your ERA CoBioTech bids.

We have prepared a frequently asked questions document. to help you understand more about the data management component of the grant.

To prepare the written data management section we have prepared:

  1. Minimum data management planning checklist
  2. A boiler plate text that you can use and modify.

We encourage people who want to include us to speak directly with us. You can contact us at community@fair-dom.org.
Webinar video

Slides from the webinar

 

 

FAIRDOM will be at the European Open Science Cloud Summit (12th June 2017)

FAIRDOM will be attending the European Open Science Cloud (EOSC) Summit today, to help with generating a number of concrete statements related to how the EOSC should be implemented.

The event aims to:

  • take stock of the progress made so far
  • give stakeholders the opportunity to review the Commission’s vision for the European Open Science Cloud
  • build consensus on the implementation plan and next steps

Carole Goble will be representing FAIRDOM, and our community. She will be speaking between 11:50 and 13:00 European Time, and you can catch a live stream of the whole event here:
https://webcast.ec.europa.eu/european-open-science-cloud-summit

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.