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Reproducible research workflows in the EOSC Federation

Sesink, Laurents; den Heijer, Cornelis

Publisher
Zenodo
DOI
10.5281/zenodo.17296180
Repository
zenodo.org
Language
en

Abstract

The European Open Science Cloud (EOSC) is no longer just a vision – it has become tangible, with an EU node up and running and national nodes in development. But what does this federation mean for researchers in practice, and how can it support reproducibility? In this workshop, we will take you on a guided tour of the EOSC Federation. You will learn what EOSC Nodes are and how they connect services, data, and tools across Europe. We then explore how Virtual Research Environments (VREs) within a Node can support collaborative and reproducible research, lowering technical barriers while opening new possibilities for sharing workflows. A key part of the workshop is dedicated to hands-on exploration. Together, we will work with a reproducibility workflow in a VRE and use RO-Crate, a lightweight format to capture and package research processes. This will allow you to see for yourself how workflows can be shared, understood, and re-run by others — a practical step towards making reproducibility both achievable and sustainable. You don’t need to be a technical expert to join; curiosity and interest in reproducible research are enough. By the end of the session, you’ll have a clearer picture of how the EOSC Federation can support your work and how tools like RO-Crate and VREs can help make research more transparent, reusable, and impactful.

Full text

Laurents Sesink - Programma manager Innovation Zone Open Science –SURF Kees den Heijer –National Liaison DCC Implementation Network 6 October 2025, DCC-PO and LCRDM Networking Day Title slide Reproducible research workflows in the EOSC Federation TEXT SLIDE (100%)TEXT SLIDE (100%) Agenda ▪What is the EOSC Federation ▪Hands-on with reproducible workflow ▪Discussion and evaluation 2 https://edu.nl/ebjt7 TEXT SLIDE (100%)TEXT SLIDE (100%) What is the EOSC Federation A Web of FAIR digital objects (e.g. data, publications and software) and Services’ for science in Europe. A multi-disciplinary environment where researchers can publish, find and re-use data, tools and services, enabling them to better conduct their work. Governed and developed by the EC, European member states and associated countries and the community (research performing institutes, service providers, funders). 3 TEXT SLIDE (100%)TEXT SLIDE (100%) Organisations involved in the Netherlands e-infrastructures Best practices & support Domain specific Research Infrastructures Research performing, supporting and funding organisations Make Open Science the norm ⚫Technical and Semantic Interoperability TF ⚫Long term Data Retention TF ⚫EOSC Federation Handbook writers’ team ⚫FAIRCORE4EOSC, FAIR-IMPACT, EOSC-ENTRUST, AARC-TREE EOSC Related activities EOSC NL WG EOSC-A Members/observers 4 TEXT SLIDE (100%)TEXT SLIDE (100%) EOSC is a federation (system of systems) 5 An open, trusted, federation of infrastructures It provides access to existing Research Infrastructures in Europe It will enable circa 2 million European researchers to store, share, process, analyze, and reuse research digital objects TITLE ONLY EOSC EU Node TITLE ONLY EOSC EU node Access to data, storage, compute and analysis tools Step 1. Search for data in the EOSC EU node Step 5. Upload your data in the EOSC EU node Step 6. Create a Jupyter Notebook in the EOSC EU node Step 7. Start analysing your data Step 2. Login the EOSC EU node Step 3. Check you free credits Step 4. Create a VRE TITLE ONLY EOSC EU Node: https://open-science-cloud.ec.europa.eu Step 1 Search for data in the EOSC EU node TITLE ONLY Acces to Storage, Compute, Notebooks Step 2 Login the EOSC EU node Step 3 Check your free credits TITLE ONLY 2) Search for dataset in EOSC EU Node https://open-science-cloud.ec.europa.eu/resources/all Dataset for this workshop TITLE ONLY 3) Explore metadata of the dataset Note the RO-Crate Metadata,a lightweight format to capture and package research processes TITLE ONLY 4) Log in on EOSC SURF Node https://eosc.nl TITLE ONLY 5) Create new workspace "Reproducibility VRE" Workspaces have been prepared for this workshop, watch the DEMO TITLE ONLY 5) Select collaborative organisation for new workspace Workspaces have been prepared for this workshop, watch the DEMO TITLE ONLY 5) Select wallet for new workspace Workspaces have been prepared for this workshop, watch the DEMO TITLE ONLY 5) Select catalog item "Reproducibility VRE" for new workspace Workspaces have been prepared for this workshop, watch the DEMO TITLE ONLY 5) Select cloud, operating system and specs for new workspace Workspaces have been prepared for this workshop, watch the DEMO TITLE ONLY 5) Set final details, including RO-Crate for new workspace Workspaces have been prepared for this workshop, watch the DEMO TITLE ONLY 5) Create new workspace "Reproducibility VRE" Workspaces have been prepared for this workshop, watch the DEMO The RO-Crate Metadata forms the recipe for the data and software in this Reprodocibility VRE TEXT SLIDE (100%)TEXT SLIDE (100%) 11) Re-run all cells in the Notebook [*] means “this cell is running or waiting to run — the kernel is busy.” TEXT SLIDE (100%)TEXT SLIDE (100%) 12) Review the results, scan for failures Note the numbers in square brackets next to the cells, indicating the execution order TEXT SLIDE (100%)TEXT SLIDE (100%) 13) Run the remaining notebooks For each repeat steps 9-12: •Check if kernel is set to reproducibility oIf not: switch kernel •Take a look at the notebook (scroll down) •Re-run the notebook oRun -> Run All Cells •Review the results, scan for failures TEXT SLIDE (100%)TEXT SLIDE (100%) Discussion and evaluation