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28 Publications visible to you, out of a total of 28
Publication of the usage of EuroScienceGateway by multiple communities

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Description Documentation of the cross-domain adoption of the EuroScienceGateway (ESG) project, showcasing how Galaxy was used and extended to meet the data analysis needs of researchers across …ers across biodiversity, climate science, astrophysics, materials science, and biomedical domains. This record outlines ESG’s impact on the onboarding of diverse scientific communities, enabling scalable, reproducible, and FAIR-compliant workflows. Through targeted outreach, infrastructure integration, and community-driven tool development, the project successfully onboarded new user groups and demonstrated Galaxy’s adaptability across multiple scientific verticals. Over 800 tools were integrated into Galaxy during the past 3 years, and dozens of reusable workflows were published to support sensitive data handling, high-throughput image analysis, simulation environments, and federated compute. The deliverable documents use cases, domain-specific onboarding models, training efforts, and collaborative success stories, including the development of the Galaxy Codex and strategic alignment with EOSC, ELIXIR, and NFDI initiatives. Project: EuroScienceGateway was funded by the European Union’s Horizon Europe programme (HORIZON-INFRA-2021-EOSC-01) under grant agreement number 101057388. Document: D5.2 Publication of the usage of EuroScienceGateway by multiple communities Work Package: Work Package 5. Community engagement, adoption and onboarding Tasks: Task 5.1 Biodiversity and Climate Science Task 5.2 Materials Science Task 5.3 Astrophysics Task 5.4 Mentoring and onboarding new communities Lead Beneficiary: University of Oslo (UiO) Contributing Beneficiaries: UiO, ALU-FR, CNRS, UNIFI, UKRI, EPFL, UP, BSC

Authors: Armin Dadras, Denys Savchenko, Andrii Neronov, Volodymyr Savchenko, Nikolay Vazov, Jean Iaquinta, Eva Alloza, María Chavero Díez, Anthony Bretaudeau

Date Published: 18th Aug 2025

Publication Type: Tech report

Publication on the Pulsar Network, integrated in workflow management systems

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Description Documentation of the design, deployment, and operationalization of the European Pulsar Network, developed within the EuroScienceGateway (ESG) project. This deliverable outlines how the …w the Pulsar Network enables scalable, federated, and interoperable remote job execution across European Galaxy servers and compute infrastructures. This record showcases the technical architecture, automation strategies, and monitoring solutions behind the distributed execution framework, supporting reproducible workflows and efficient resource sharing. The network connects 13 Pulsar endpoints across 10 countries, integrated with six national Galaxy servers and the European Galaxy server. Deployments span public clouds, institutional HPCs, and EOSC resources, unified under a secure, open-source infrastructure stack using Terraform, Ansible, RabbitMQ, CVMFS, and SABER. The deliverable demonstrates how ESG addressed interoperability and scalability challenges through open infrastructure tooling, cross-institutional coordination, and continuous monitoring. It provides a replicable model for distributed compute resource integration and highlights Galaxy's extensibility in federated scientific computing. Project: EuroScienceGateway, funded by the European Union’s Horizon Europe programme (HORIZON-INFRA-2021-EOSC-01) under grant agreement number 101057388. Document: D3.2 Publication on the Pulsar Network, integrated in workflow management systems Work Package: Work Package 3. Pulsar Network: Distributed heterogeneuos compute Tasks: - Task 3.1 Develop and maintain an Open Infrastructure-based deployment model for Pulsar endpoints - Task 3.2 Add GA4GH Task Execution Service (TES) API to Pulsar - Task 3.3 Build a European-wide network of Pulsar sites - Task 3.4 Add TES support to WfExS (Workflow Execution Service) - Task 3.5 Developing and maintaining national or domain-driven Galaxy servers Lead Beneficiary: CNR Contributing Beneficiaries: CNR, INFN, ALU-FR, CNRS, CESNET, UiO, UB, EPFL, AGH/AGH-UST, BSC, VIB, IISAS, TUBITAK, UNIMAN

Authors: Armin Dadras, Marco Antonio Tangaro

Date Published: 1st Aug 2025

Publication Type: Tech report

Publication on the smart job scheduler implementation

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Project: EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) …KRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963. Document: D4.2 Publication on the smart job scheduler implementation Work Package: Work Package 4. Building blocks for a sustainable operating model. Task: - Task 4.3 Implement a smart job-scheduling system across Europe Lead Beneficiary: EGI Contributing Beneficiary: ALU-FR, CESNET, EGI, UiO, and VIB Executive Summary Galaxy is currently using the Total Perspective Vortex (TPV) to schedule millions of jobs for hundred thousand users globally. While TPV has proven to be a robust meta-scheduling tool for Galaxy in the last years, there are areas of improvement that have been addressed in the EuroScienceGateway project: - Gathering live usage metrics from across the distributed computing endpoints connected to Galaxy in order to distribute the load across all sites. - Adding latitude and longitude attributes to data stores and computing endpoints to allocate jobs as close as possible to the location of the data. - Visualizing job distribution across sites with an intuitive dashboard. As a result the EuroScienceGateway project has developed two new tools: - TPV Broker for the efficient meta-scheduling of jobs taking into account real-time usage metrics and data-locality information - Galaxy Job Radar: a web dashboard to easily visualize the allocation of jobs across all sites The EuroScienceGateway project has significantly improved the meta-scheduling of jobs for Galaxy, resulting in less waiting times for users to see their job completed and improving resource utilization across all sites.

Authors: Abdulrahman Azab, Sanjay Kumar Srikakulam, Paul De Geest, Tomáš Vondrák, Björn Grüning, Mira Kuntz, Enol Fernandez-del-Castillo, Sebastian Luna-Valero

Date Published: 27th Feb 2025

Publication Type: Tech report

Recording provenance of workflow runs with RO-Crate

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Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to … address this need, providing representations of workflow plans and their executions as well as means of packaging the resulting information for archiving and sharing. However, existing approaches tend to lack interoperable adoption across workflow management systems. In this work we present Workflow Run RO-Crate, an extension of RO-Crate (Research Object Crate) and Schema.org to capture the provenance of the execution of computational workflows at different levels of granularity and bundle together all their associated objects (inputs, outputs, code, etc.). The model is supported by a diverse, open community that runs regular meetings, discussing development, maintenance and adoption aspects. Workflow Run RO-Crate is already implemented by several workflow management systems, allowing interoperable comparisons between workflow runs from heterogeneous systems. We describe the model, its alignment to standards such as W3C PROV, and its implementation in six workflow systems. Finally, we illustrate the application of Workflow Run RO-Crate in two use cases of machine learning in the digital image analysis domain.

Authors: Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno P. Kinoshita, Stian Soiland-Reyes

Date Published: 10th Sep 2024

Publication Type: Journal

Scaling Scientific Workflows in Europe: Architecture and Deployment of the Galaxy-Pulsar Computational Network

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Description This preprint outlines the development and deployment of the European Pulsar Network (EPN)—a federated, scalable architecture enabling distributed job execution across national and European …opean Galaxy instances. Built within the Horizon Europe EuroScienceGateway project, the EPN leverages the Galaxy workflow system and the Pulsar job execution service to offload computational workloads to remote endpoints seamlessly and securely. The work introduces an Open Infrastructure (OI) framework that automates provisioning, deployment, and monitoring using Terraform, Ansible, and Jenkins. The pre-print highlights deployments across thirteen Pulsar nodes and six national Galaxy portals, illustrating how the EPN supports reproducible, FAIR-aligned data analysis while abstracting infrastructure complexity for researchers.

Authors: Marco Antonio Tangaro, Stefano Nicotri, Björn Grüning, Sanjay Kumar Srikakulam, Armin Dadras, Oana Kaiser, Mira Kuntz, Anthony Bretaudeau, Paul De Geest, Sebastian Luna-Valero, María Chavero Díez, José María Fernández González, Salvador Capella-Gutierrez, Josep Lluís Gelpí, Jan Astalos, Boris Jurič, Miroslav Ruda, Łukasz Opioła, Hakan Bayındır, SILVIA GIOIOSA, Gaetanomaria De Sanctis, Federico Zambelli

Date Published: 7th Aug 2025

Publication Type: Unpublished

Ten simple rules for making a software tool workflow-ready

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Workflows have become a core part of computational scientific analysis in recent years. Automated computational workflows multiply the power of researchers, potentially turning “hand-cranked” data …data processing by informaticians into robust factories for complex research output. However, in order for a piece of software to be usable as a workflow-ready tool, it may require alteration from its likely origin as a standalone tool. Research software is often created in response to the need to answer a research question with the minimum expenditure of time and money in resource-constrained projects. The level of quality might range from “it works on my computer” to mature and robust projects with support across multiple operating systems. Despite significant increase in uptake of workflow tools, there is little specific guidance for writing software intended to slot in as a tool within a workflow; or on converting an existing standalone research-quality software tool into a reusable, composable, well-behaved citizen within a larger workflow. In this paper we present 10 simple rules for how a software tool can be prepared for workflow use.

Authors: Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble

Date Published: 24th Mar 2022

Publication Type: Journal

The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

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A key limiting factor in organising and using information from physical specimens curated in natural science collections is making that information computable, with institutional digitization tending … to focus more on imaging the specimens themselves than on efficiently capturing computable data about them. Label data are traditionally manually transcribed today with high cost and low throughput, rendering such a task constrained for many collection-holding institutions at current funding levels. We show how computer vision, optical character recognition, handwriting recognition, named entity recognition and language translation technologies can be implemented into canonical workflow component libraries with findable, accessible, interoperable, and reusable (FAIR) characteristics. These libraries are being developed in a cloud- based workflow platform—the ‘Specimen Data Refinery’ (SDR)—founded on Galaxy workflow engine, Common Workflow Language, Research Object Crates (RO-Crate) and WorkflowHub technologies. The SDR can be applied to specimens’ labels and other artefacts, offering the prospect of greatly accelerated and more accurate data capture in computable form. Two kinds of FAIR Digital Objects (FDO) are created by packaging outputs of SDR workflows and workflow components as digital objects with metadata, a persistent identifier, and a specific type definition. The first kind of FDO are computable Digital Specimen (DS) objects that can be consumed/produced by workflows, and other applications. A single DS is the input data structure submitted to a workflow that is modified by each workflow component in turn to produce a refined DS at the end. The Specimen Data Refinery provides a library of such components that can be used individually, or in series. To cofunction, each library component describes the fields it requires from the DS and the fields it will in turn populate or enrich. The second kind of FDO, RO-Crates gather and archive the diverse set of digital and real-world resources, configurations, and actions (the provenance) contributing to a unit of research work, allowing that work to be faithfully recorded and reproduced. Here we describe the Specimen Data Refinery with its motivating requirements, focusing on what is essential in the creation of canonical workflow component libraries and its conformance with the requirements of an emerging FDO Core Specification being developed by the FDO Forum.

Authors: Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes

Date Published: 7th Mar 2022

Publication Type: Journal

WorkflowHub: a registry for computational workflows

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The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of … analysis and descriptions of processing steps, workflows should be reproducible, reusable, adaptable, and available. Workflow sharing presents opportunities to reduce unnecessary reinvention, promote reuse, increase access to best practice analyses for non-experts, and increase productivity. In reality, workflows are scattered and difficult to find, in part due to the diversity of available workflow engines and ecosystems, and because workflow sharing is not yet part of research practice. WorkflowHub provides a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR). By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.

Authors: Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José M. Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble

Date Published: 1st Dec 2025

Publication Type: Journal

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