Monthly Archives: January 2017

ERA CoBioTech webinars

ERA CoBioTech, in collaboration with FAIRDOM, will provide data and model management support to all participating projects.

In accordance with the ERA CoBioTech call, the full proposal stage will require a section of the application dedicated to data and model management.

To help applicants prepare their proposals, and to learn more about the data management needs of the participating projects, FAIRDOM will host a series of webinars.

Dates for webinars will be:

Thu, Feb 2, 2017 3:00 PM – 5:00 PM CET

Tue, Feb 7, 2017 11:00 AM – 1:00 PM CET

To register for the webinar(s) please go to

The webinars will be organised as a 1 hour session and cover what FAIRDOM and its central data management services offer, what FAIRDOM would need in terms of collaboration to deliver the best service possible, as well as a checklist of data and model management topics to be covered in the proposal. This informative session will then be followed by an hour open for questions, discussions, suggestions with the possibility for scheduling breakout sessions.

SEEK Version 1.2 released

The FAIRDOM team are pleased to announce a new version of SEEK, version 1.2, available to download and install.

Version 1.2 includes a major reimplementation and design of support for Samples, along with many other improvements.

  • developed from discussions within the FAIRDOM-ELIXIR Samples Club
  • sample types with user-defined sets of attributes and attribute types
  • sample types defined manually or from a spreadsheet template
  • samples entered manually or read from a spreadsheet
  • validation of samples against the sample type
  • relations between samples and also to internal and external resources

From this version onwards SEEK is also available through Docker. For details, please see our SEEK Docker guide.

Full details on the improvements included in 1.2 can be found on the SEEK website

Upgrading an existing SEEK to version 1.2 follows the standard steps. Always remember to backup before doing an upgrade!

Did you miss out on our first webinar of 2017? Catch up here!

Did you miss out on our first webinar “Building a training material portal: BioSchemas and metadata scraping”, by guest speaker Niall Beard from ELIXIR-UK?

You can catch up on the webinar here:

and sign up for future webinars here:

To find out more about our webinar series please visit:

Register for FAIRDOM’s 2017 Webinar Series

After a hugely successful 2016 series, FAIRDOM will be launching its 2017 Webinar series on Thursday 19th January at 2pm GMT.

The webinar series will be of interest to students, researchers, project investigators, lab managers, institutions, publishers, data providers….anyone with data or models to manage.

Our first speaker will be Niall Beard representing ELIXIR-UK. He will be talking about “Building a training material portal: ELIXIR TeSS, BioSchemas and metadata scraping”. 

For any discipline, identifying high quality training materials is difficult. They are often spread across different institutional websites, personal blogs, or stored in archives. This means you have to know exactly what you are looking for, and where to find it. However, for many, training occurs when the person knows little about the subject they wish to train in. This makes it difficult to know what material they need to look for. Once it is identified, it is also difficult to know what quality others within the community rate that material. To solve this problem for European Bioinformatics, we have generated the TeSS Portal. TeSS aggregates links to disparate training materials and events scattered around the institutional websites of ELIXIR Nodes and other content providers (GOBLET, Software and Data Carpentry, EBI TrainOnline, Genome3D, on-course, and more.), making them centrally discoverable and searchable. Training resources within TeSS can be collected and arranged into packages and/or training workflows, forming graphical representations of scientific pipelines in order to organise resources into easily navigable views. Aggregation of training content happens automatically through a set of custom-made nightly-run scraper scripts. Scrapers use a number of techniques to extract information: HTML-scraping and APIs had been the predominant methods, but are either temperamental or scarcely found respectively. More recently we have focused on parsing structured mark-up data. The TeSS team, through the Bioschemas group, have been heavily involved in developing specifications for Life science training resources and promoting their adoption”

Future speakers include

16th March, Caterina Barillari (ETH Zürich). “High-throughput data management: openBis”
20th April, Veerle Van den Eynden (UK Data Archive, UK) and Gareth Knight (London School of Hygiene and Tropical Medicine. “Open Science attitudes and practices among Wellcome and ESRC funded researchers”
18th May, Carole Goble (University of Manchester, UK), “FAIRDOM”
15th June, Bjoern Gruening, “Conda and Containers for a sustainable bioinformatic infrastructure”.
20th July, MAtthew Pocock (Turing Ate My Hamster LTD), “ShortBOL: A shorthand for synthetic biology design”.

To sign up to the webinar series please visit: 

To find out more about Niall Beard and his webinar you can visit:

The webinars will run on the third Thursday of each month at 2pm GMT. 

To find out more about the webinar series you can visit:

We’re looking forward to seeing you there!

A Data Citation Roadmap for Scholarly Data Repositories

Martin Fenner from DataCite, and collaborators have just published “A Data Citation Roadmap for Scholarly Data Repositories”

The article “presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles (Data Citation Synthesis Group, 2014), a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Early Adopters Expert Group, part of the Data Citation Implementation Pilot (DCIP) project (FORCE11, 2015), an initiative of and the NIH BioCADDIE (2016) program. The roadmap makes 11 specific recommendations, grouped into three phases of implementation: a) required steps needed to support the Joint Declaration of Data Citation Principles, b) recommended steps that facilitate peer-reviewed) is the author/funder. It is made available under a CC-BY 4.0 International license. bioRxiv preprint first posted online Dec. 28, 2016; doi: The copyright holder for this preprint (which was not 2 article/data publication workflows, and c) optional steps that further improve data citation support provided by data repositories.”

For more information please visit: