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Galaxy goes Research Data Infrastructure

The Galaxy Europe Team active at NFDI's CoRDI (Karlsruhe, Germany, Sep 12th to 14th)

Being a well-known infrastructure for scientific data handling, Galaxy gets increasingly recognized as a powerful solution for research data management (RDM). Thus, it simply had to be represented at CoRDI, the first 'Conference on Research Data Infrastructure' in Karlsruhe/Germany. Starting from Sep 12th, the three-day event was geographically close to the Freiburg Team, and organized by NFDI, the National initiative for Research Data Infrastructure. NFDI now involves 27 consortia from three funding rounds and various scientific fields; it aims for both streamlining German RDM efforts, but also with European initiatives like EOSC. Obviously, 'joining forces' is a principle from Galaxy's center of gravity, and less obviously, Galaxy is already participating in two projects from the NFDI space...

DataPLANT has been initiated in October 2020 and addresses the particular needs of the plant science community. Accordingly, the consortium is supported with adaptations of the Galaxy platform: tools, workflows, data types and training material have been improved. Scientists from other fields might have spotted the respective GTN materials bundled as plant module, which is dedicated in particular to plant transcriptomics.

NFDI4BIOIMAGE has been kicked off in March 2023, and aims for improved handling of biological imaging data. Being traditionally centric to datatypes, assays or imaging platforms, the improvement of interoperability is on the consortium's agenda. Galaxy again provides the respective infrastructure for image data handling, improving e.g. the toolset of the imaging.usegalaxy.eu subdomain.

At CoRDI, usegalaxy.eu was represented with two posters and two talks:

On Day 2, Sanjay presented the poster "Conda, Container and Bots - How to build and maintain tool dependencies in workflows and training materials" (PDF), and was supported by Björn and Sebastian. Lively discussions spinned up with researchers from various fields. The sophisticated, largely bot-driven CI/CD system of Galaxy, building on Conda and Planemo, was much appreciated and regarded as a very professional approach, including community-control, being open source and free of costs. For more details, check out the Planemo paper (Bray et al. 2023), which we presented in this blog post.

At the same time, Tunc presented our second poster on "Interactive Tools (IT) in Galaxy: Combining synchronous and asynchronous workflows" (PDF), supported by Björn. The interest was high, too, and several discussions came up, both on architectural aspects and the scope of applications.

On Day 3, Björn gave a talk on GTN and TIaaS ("FAIR and Scalable Education - The Galaxy Training Network (GTN) and a Training Infrastructure as a Service (TIaaS)"). Despite being close to lunch, the audience of the education-related session was pleased to be provided with a 15 minutes presentation of GTN's principles, its grown contents, and not least the great community behind it. While comparable platforms address particular fields or are yet limited on the technical level or the available contents, GTN convinced with its maturity as a result of years of development. Proud to say that questions from the audience also addressed immediately how to effectively contribute. GTN folks, be prepared for new colleagues and contents :).

Right after lunch, Sebastian presented an overview on "Galaxy and RDM"; after having introduced Galaxy as a field-agnostic platform and RDMkit's data life cycle, the alignment with Galaxy's features were sketched, underlining that Galaxy covers the entire cycle. Moreover, Galaxy improved in connecting to well-known interoperability resources like WorkflowHub and Zenodo. Standards are obviously key here, and the adoption of standardized exchange formats like RO-Crate for both importing and exporting data and metadata rose considerable interest.

Other unordered highlights from Karlsruhe: around 681 participants onsite, 84 talks in up to four parallel sessions, 105 posters, a very good organization team, York Sure-Vetter ("lead") and Carole Goble (Program Chair) in an excellent mood, and Björn holding a chair together with Juliane Fluck for the "Life sciences" session. If you are ever in Karlsruhe: do not miss the Light Festival show at the Castle. For the organizers' wrap up, click here.

We are looking forward to continued and extended cooperation in and with the NFDI space. Note: CoRDI will return in 2025, and NFDI will join forces at a common conference with EOSC next year in Berlin (Oct 21-23; comp. note here, bottom of the page). Hope to see as many of you as possible there!