Author Archives: Ulrike Wittig

Keynote talk “Faring with FAIR” by Carole Goble at GMDS Workshop


Carole Goble is giving a keynote talk about “Faring with FAIR” at the GMDS Workshop “FAIRe Data Infrastructures” on Thursday, October 15th, 2020.

Abstract of the talk:

Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines. Many of the authors (including myself) came from biomedical and associated communities. The paper succeeded in its aim, at least at the policy, enterprise and professional data infrastructure level. Whether FAIR has impacted the researcher at the bench or bedside is open to doubt. It certainly inspired a great deal of activity, many projects, a lot of positioning of interests and infrastructure initiatives such as FAIRDOM. COVID has injected impetus and urgency to the FAIR cause (good), highlighted its politicisation (not so good) and the need to reassure communities that FAIR for health related data is not a contradiction with data privacy. In this talk I’ll reflect on how we are faring with FAIR: as one of the original authors; as a FAIR infrastructure developer for the biomedical sector and as a veteran of FAIR before we had the principles.

de.NBI Course: “Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK”

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks.

Date: September 21-23, 2020

More details and registration: Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK

COVID-19 Disease Map on FAIRDOMHub

FAIRDOM helps to collect knowledge about the molecular mechanisms of COVID-19 and established a project in FAIRDOMHub for the COVID-19 Disease Map:


The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence for virus-host interaction mechanisms specific to the SARS-CoV-2. In the project lists of contributors, data and computational models, and literature is shared.


FAIRDOMHub and the data management support for the COVID-19 disease map gets featured in Nature Scientific Data

FAIR Data Management for Projects: FAIR at the first Mile

FAIRDOM members Carole Goble, Wolfgang Müller & Frederik Coppens ran an ELIXIR workshop at the all ELIXIR hands meeting in Lisbon, 17 – 20 June 2019. Its purpose was to

* Share information on ongoing projects and (strategic) plans within ELIXIR touching on ‘FAIR at the First Mile’ (local data management).

* To bring together Nodes, Platforms and Communities along with other organisations (like FAIRDOM) to share and propose best practices, platforms and joint work for FAIR data management for projects supported by the Nodes.

* To discuss plans for for ELIXIR CONVERGE (ELIXIR’s INFRADEV3 proposal), EOSC-Life Plant A+ pilot and the EIP Strategic Plan Task 2 ‘Interoperability with a purpose’.

After an introduction by Frederk Coppens, deputy Head of Node (HoN) of Belgium describing ELIXIR-CONVERGE, Pinar Alper from Luxembourg described their human data setup which is tailored to meeting complex data protection needs. Inge Jonassen, HoN of Norway described the FAIRDOM/NELS setup run by ELIXIR-NO.

After a talk on FAIRDOM for first-mile data management by Wolfgang Müller, describing some approaches to be used in the EOSC-Live pilot Plant A+, the workshop closed with asession about the Interoperability Platform strategic Plan Task 2, the interoperabiltiy for ELIXIR Communites and Nodes.

Ghent FAIRDOM workshop, 11-12 June 2019

Frederik Coppens of VIB invited institutional data managers from the Belgian Flanders region, as well as FAIRDOM team and users to Ghent in order to discuss FAIRDOM data management and possible future collaboration.

The workshop started out with a presentation session in which the participating institutions presented their planned use case scenarios.

Katy Wolstencroft from Uni Leiden presented the early history of FAIRDOM, the use cases that shaped FAIRDOM and SEEK.  After a discussion of the need of the visiting institution, Fatemeh Zamanzad Ghavidel from Bergen (Digital Life, ELIXIR Norway) presented their use of FAIRDOM together with NeLS, the Norwegian e-Infrastructure for the Life Sciences. Then Wolfgang Müller of FAIRDOM/LiSyM/de.NBI described a variety of use cases for FAIRDOM in projects.

Then, Stuart Owen presented the FAIRDOM solution for a concrete scenario provided by Frederik Coppens. This scenario involved running Galaxy from within FAIRDOM, the use of sample types in SEEK, as well as the extraction of metadata. Wolfgang Müller presented Jupyter Notebooks running from within SEEK, as well as the use of openRefine for creating bespoke data transformation solutions.

The day finished with breakout discussions about a variety of topics from development to community management.

On the second day, pathways to collaboration were discussed in more depth.