Publications

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19 Publications visible to you, out of a total of 19
An Ecosystem of Services for FAIR Computational Workflows

Abstract (Expand)

Computational workflows, regardless of their portability or maturity, represent major investments of both effort and expertise. They are first class, publishable research objects in their own right. … They are key to sharing methodological know-how for reuse, reproducibility, and transparency. Consequently, the application of the FAIR principles to workflows [goble_2019, wilkinson_2025] is inevitable to enable them to be Findable, Accessible, Interoperable, and Reusable. Making workflows FAIR would reduce duplication of effort, assist in the reuse of best practice approaches and community-supported standards, and ensure that workflows as digital objects can support reproducible and robust science. FAIR workflows also encourage interdisciplinary collaboration, enabling workflows developed in one field to be repurposed and adapted for use in other research domains. FAIR workflows draw from both FAIR data [wilkinson_2016] and software [barker_2022] principles. Workflows propose explicit method abstractions and tight bindings to data, hence making many of the data principles apply. Meanwhile, as executable pipelines with a strong emphasis on code composition and data flow between steps, the software principles apply, too. As workflows are chiefly concerned with the processing and creation of data, they also have an important role to play in ensuring and supporting data FAIRification. The FAIR Principles for software and data mandate the use of persistent identifiers (PID) and machine actionable metadata associated with workflows to enable findability, reusability, interoperability and reusability. To implement the principles requires a PID and metadata framework with appropriate programmatic protocols, an accompanying ecosystem of services, tools, guidelines, policies, and best practices, as well the buy-in of existing workflow systems such that they adapt in order to adopt. The European EOSC-Life Workflow Collaboratory is an example of such a digital infrastructure for the Biosciences: it includes a metadata standards framework for describing workflows (i.e. RO-Crate, Bioschemas, and CWL), that is managed and used by dedicated new FAIR workflow services and programmatic APIs for interoperability and metadata access such as those proposed by the Global Alliance for Genomics and Health (GA4GH) [rehm_2021]. The WorkflowHub registry supports workflow Findability and Accessibility, while workflow testing services like LifeMonitor support long-term Reusability, Usability and Reproducibility. Existing workflow management systems/languages and packaging solutions are incorporated and adapted to promote portability, composability, interoperability, provenance collection and reusability, and to use and support these FAIR services. In this chapter, we will introduce the FAIR principles for workflows, the connections between FAIR workflows, and the FAIR ecosystems in which they live, using the EOSC-Life Collaboratory as a concrete example. We will also introduce other community efforts that are easing the ways that workflows are shared and reused by others, and we will discuss how the variations in different workflow settings impact their FAIR perspective.

Authors: Sean R. Wilkinson, Johan Gustafsson, Finn Bacall, Khalid Belhajjame, Salvador Capella, José María Fernández González, Jacob Fosso Tande, Luiz Gadelha, Daniel Garijo, Patricia Grubel, Björn Grüning, Farah Zaib Khan, Sehrish Kanwal, Simone Leo, Stuart Owen, Luca Pireddu, Line Pouchard, Laura Rodriguez-Navas, Beatriz Serrano-Solano, Stian Soiland-Reyes, Baiba Vilne, Alan Williams, Merridee Ann Wouters, Frederik Coppens, Carole Goble

Date Published: 21st May 2025

Publication Type: InBook

Applying the FAIR Principles to computational workflows

Abstract

Not specified

Authors: Sean R. Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick Juty, Sehrish Kanwal, Farah Zaib Khan, Johannes Köster, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole Goble

Date Published: 1st Dec 2025

Publication Type: Journal

Bring Your Own Infrastructure

Abstract (Expand)

Development of the needed extensions of the EuroScienceGateway components (Pulsar and Galaxy) to automate and facilitate the integration of user provided computing and storage resources. 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) under the UK government’s Horizon Europe funding guarantee grant number 10038963. Document: D4.1 Bring Your Own Infrastructure Work Package: Work Package 4. Building blocks for a sustainable operating model. Task: - Task 4.1 Bring Your Own Compute (BYOC) - Task 4.2 Bring Your Own Storage (BYOS) Lead Beneficiary: EGI Contributing Beneficiary: AGH-UST, ALU-FR, EGI, INFN, and VIB Executive Summary This deliverable presents the activities carried out in tasks 4.1 “Bring Your Own Compute (BYOC)” and 4.2 “Bring Your Own Storage (BYOS)”, under Work Package 4 “Building blocks for a sustainable operating model”. The overall goal of tasks 4.1 and 4.2 is to make it easier for Galaxy users to connect their accounts in Galaxy to existing, externally managed compute and storage resources. The benefits are twofold: 1) Galaxy administrators do not need to operate and maintain additional IT infrastructure and 2) Galaxy users get extra capacity to execute workflows that are beyond their assigned quotas in Galaxy.

Authors: Maiken Pedersen, Sanjay Kumar Srikakulam, Paul De Geest, Enol Fernandez-del-Castillo, Andrea Cristofori, Sebastian Luna-Valero, Marco Antonio Tangaro, Stefano Nicotri

Date Published: 26th Aug 2024

Publication Type: Tech report

Community onboarding cookbook published

Abstract (Expand)

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) … under the UK government’s Horizon Europe funding guarantee grant number 10038963. Document: D 5.1 Community onboarding cookbook published Work Package: Work Package 5: Community engagement, adoption and onboarding Task: Task 5.4 Mentoring and onboarding new communities Lead Beneficiary: University of Oslo Contributing Beneficiary: All partners Executive Summary The onboarding cookbook is a set of documents describing the creation of the Galaxy communities of practice called Special Interest Groups (SIG). It outlines the necessary steps which shall precede every SIG creation : search for already existing SIGs which match the required profile; clear definition of the future SIG's goals; setup of SIG's administrative bodies and routines; planning of future publications and training. The Cookbook also lists the minimum of prerequisites required before the creation of a new SIG. The goal of these recommendations is to empower the SIG creators to run a Galaxy community . Success stories of already onboarded communities with different levels of maturity are shared, focusing on their experience in using Galaxy and building their SIGs (Milestone 12 - Interim report on the activities of the 3 early adopters and assessment of the take up by their respective communities).

Author: Vazov Nikolay

Date Published: 29th Feb 2024

Publication Type: Journal

D3.1 Operations documentation on the Open Infrastructure deployment

Abstract (Expand)

Development of the Open Infrastructure and Pulsar Network to support distributed job execution and scalable Galaxy deployments across Europe. Project: EuroScienceGateway was funded by the European Union …Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963. Document: D3.1 Operations documentation on the Open Infrastructure deployment Work Package: Work Package 3. Pulsar Network: Distributed heterogeneous compute. Tasks: - Task 3.1 Develop and maintain an Open Infrastructure based deployment model for Pulsar endpoints. - Task 3.3 Build a European-wide network of Pulsar sites. - Task 3.5 Developing and maintaining national or domain-driven Galaxy servers. Lead Beneficiary: INFN Contributing Beneficiary: INFN, ALU-FR, CNRS, CESNET, UiB, BSC, VIB, IISAS, TUBITAK and CNR Executive Summary Work Package 3 of the EuroScienceGateway project is divided into 5 tasks, aimed at bringing into production (TRL9) the Pulsar Network , a distributed computing network that allows public Galaxy servers to offload jobs to remote computing clusters provided by project partners. Specifically, this deliverable describes the work done in tasks 3.1, 3.2, 3.3 and 3.5. The main objectives of WP3 are: 1) to simplify the deployment and management of new Pulsar and Galaxy endpoints (T3.1 and T3.5), to make Pulsar compatible with the GA4GH TES specifications (T3.2), and to deploy new Pulsar endpoints (T3.3)

Authors: Stefano Nicotri, Marco Antonio Tangaro, Federico Zambelli, Miroslav Ruda, Ales Krenek, Björn Grüning, Sanjay Kumar Srikakulam, Anthony Bretaudeau, Sondre Batalden, María Chavero Díez, Paul De Geest

Date Published: 27th Aug 2024

Publication Type: Journal

EuroScienceGateway D2.1: Reproducible FAIR Digital Objects for Workflows

Abstract (Expand)

Description This EuroScienceGateway report gives an overview of FAIR Digital Objects (FDO), considering their use for computational workflows as scholarly objects. EuroScienceGateway has progressed the …d the technologies Signposting and RO-Crate for implementing Workflow FDOs with the registry WorkflowHub and the workflow system Galaxy, and initiated work with academic publishers to encourage workflow citation practices. Here we document how WorkflowHub supports research software best practices for workflows, and assist building FAIR Computational Workflows. Provenance of workflow executions has been made possible in an interoperable way across many workflow systems using Workflow Run Crate profiles, including from Galaxy. Finally this report explores how Workflow FDOs are exposed and can be utilised, e.g. gathered in knowledge graphs and having tighter workflow system integration.

Authors: Stian Soiland-Reyes, Eli Chadwick, Finn Bacall, Jose M. Fernandez, Björn Grüning, Hakan Bayındır

Date Published: 28th Aug 2024

Publication Type: Tech report

EuroScienceGateway D2.2: Publishing workflow enriched FDOs to EOSC

Abstract (Expand)

The concept of publishing workflows as scholarly is being recognised and practiced through repositories like WorkflowHub and principles for FAIR Computational Workflow. This deliverable describes how … the evolving landscape of the European Open Science Cloud (EOSC) can facilitate workflow publishing in a federated and distributed manner, exemplified by how workflows for Galaxy are published.

Authors: Stian Soiland-Reyes, Eli Chadwick, Armin Dadras, Björn Grüning, Catalin Condurache, Sebastian Luna-Valero, Volodymyr Savchenko

Date Published: 8th Feb 2025

Publication Type: Tech report

EuroScienceGateway MS3: Initial EuroScienceGateway workflows registered

Abstract (Expand)

WorkflowHub is a registry of computational workflows, provided as a EOSC Service by ELIXIR-UK, and used by over 200 different research projects, institutions and virtual collaborations. For this milestone … of EuroScienceGateway (ESG), the project has developed an onboarding guide for WorkflowHub and registered in WorkflowHub the initial ESG workflows that have been developed and maintained by the project.

Authors: Stian Soiland-Reyes, Björn Grüning, Paul De Geest

Date Published: 29th Feb 2024

Publication Type: Tech report

EuroScienceGateway MS6: Integrated EuroScienceGateway knowledge graph

Abstract (Expand)

Description The Workflowhub Knowledge Graph has been improved and its generation made more robust. When this work was last reported, a complete knowledge graph had been generated but several criticisms …icisms were made. The previous graph was: - Verbose and hard for a human to read or navigate - Had unresolvable URIs as root data entities - Contained many duplicate entries - Contained sparse metadata from only a single source Work has successfully been undertaken to address all of these points. The graph now uses partially resolvable, more human readable, URIs for root data entities. Steps have been added to the generation software to add metadata from additional sources (enrichment) and to remove duplicate entries (consolidation). Several areas of the codebase have been refactored and improved, to help ensure repeatability and longevity. The new knowledge graph still has areas that could be improved. Partially resolvable URIs should be migrated to fully resolvable alternatives. Further enrichment processes should be added which affords greater de-duplication.

Authors: Eli Chadwick, Oliver Woolland, Volodymyr Savchenko, Finn Bacall, Alexander Hambley, José María Fernández González, Armin Dadras, Stian Soiland-Reyes

Date Published: 1st Aug 2025

Publication Type: Tech report

Final summary of EuroScienceGateway main achievements, impacts, key results, sustainability data management and exploitation plans

Abstract (Expand)

Description This deliverable provides the final project summary of EuroScienceGateway (ESG), a Horizon Europe and EOSC initiative (Grant Agreement 101057388, Sept 2022–Aug 2025) coordinated by …ed by Albert-Ludwigs-Universität Freiburg. It summarizes ESG’s main achievements, impacts, FAIR data management, sustainability and exploitation plans, and dissemination outcomes. Technically, ESG delivered a production-grade, federated research gateway built on Galaxy and an expanded Pulsar Network, enabling scalable, data-intensive analysis across heterogeneous European compute and storage. Key innovations include Bring-Your-Own-Compute/Storage (BYOC/BYOS), a smart meta-scheduler (TPV Broker), Galaxy Job Radar dashboard, and streamlined deployment/admin tooling—altogether improving throughput, data locality, and operational transparency. The project operationalized FAIR principles for computational workflows by packaging and publishing Workflow RO-Crates with persistent identifiers via WorkflowHub, advancing EOSC interoperability. Federated AAI (e.g., EGI Check-in, LS Login, IAM4NFDI) supports secure access across institutions. ESG contributed >20 workflows, >40 tutorials, and >10 peer-reviewed publications, and collaborated with 20+ initiatives. Six national Galaxy instances and 10+ Pulsar endpoints were launched; the European Galaxy instance achieved ISO/IEC 27001 certification. Community impact was substantial: registered users on the European Galaxy portal grew from ~30,000 to >130,000, with monthly actives doubling to >6,000, underpinned by >20 online/onsite workshops and large-scale training through the Galaxy Training Network and Training-Infrastructure-as-a-Service (TIaaS). Sustainability is ensured through distributed governance, national/institutional hosting of Galaxy/Pulsar services, continued curation of workflows and training materials, and alignment with EOSC service models and funding pathways. The report closes with exploitation routes for beneficiaries and stakeholders and a record of dissemination and outreach activities across the European research ecosystem.

Authors: Armin Dadras, Oana Kaiser, Björn Grüning, Sebastian Luna-Valero, Enol Fernandez-del-Castillo

Date Published: 20th Aug 2025

Publication Type: Tech report

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