19-23 September 2022
Prague, Czech Republic
Europe/Amsterdam timezone

Exploring reference data through existing computing services for the bioinformatics community : an EOSC-Pillar use-case

20 Sep 2022, 19:00
1st floor (Vienna Andel Prague)

1st floor

Vienna Andel Prague

Poster Data Spaces Posters (presenters at poster)


Gilles Mathieu (INSERM)


Galaxy is a widely adopted workflow management system for bioinformatics, aiming to make computational biology accessible to research scientists that do not have computer programming or systems administration experience.
How can scientists connect this useful, reproducibility-oriented tool seamlessly with many data sources? How can they do so in a coherent way using different instances of Galaxy? Can they run it locally or on a secured infrastructure that handles patient data? Can they compare the results of those different scenarios?
The proposed poster presents the work done as part of one of the EOSC-Pillar project’s scientific use-cases to address those questions, achieving the following objectives:
● Allow access to reference data from different Galaxy deployments to all EOSC users.
● Facilitate the deployment of Galaxy instances in the same infrastructure hosting the data to analyse
● Provide coherency in the deployment of different Galaxy instances
● Ensure sensitive (e.g., health) data security requirements are met throughout the process
The poster describes four scientific scenarios based on concrete needs from the ELIXIR community. It also describes the technical services the use-case is relying on, namely: Laniakea (Galaxy as a service provided by IBIOM-CNR and INFN), Inserm data repository, IFB cloud Galaxy instances and the INDIGO-IAM authentication service provided by INFN. It demonstrates the interest of EOSC Pillar’s Federated Data Space (F2DS) for connecting different data sources to the Galaxy in a simple and coherent way.
The poster also highlights the need to conform to data protection regulations concerning health personal data, by deploying Galaxy in a private, secured environment while still ensuring the data analysis workflow remains similar to its public counterpart.
Finally, it shows proposed solutions to provide access to the service to all users within the EOSC community through roles management and by integrating it into a global authentication framework.

Any relevant links


Topic Data Spaces

Primary authors

Gilles Mathieu (INSERM) Mrs Yosra Sanaa (Inserm) Christophe Blanchet (French Institute of Bioinformatics - CNRS UMS3601) Mr Pietro Mandreoli (CNR-IBOM, University of Milan) Marco Antonio Tangaro (CNR) Giacinto Donvito (INFN) Mrs Nadina Foggetti (INFN) Marica Antonacci (INFN) Mrs Marwa Belhaj Salem (Inserm)


Mrs Laura Burlot (French Institute of Bioinformatics (IFB)) Mr Jonathan Lorenzo (French Institute of Bioinformatics (IFB)) Mr Daniele Colombo (University of Milan) Federico Zambelli (CNR (ELIXIR-ITA)) Mr David Salgado (Inserm, Aix-Marseille University)

Presentation Materials