Galaxy a FAIR-by-design platform: Bridging analysis and research data management across disciplines

Galaxy [1] is more than a data analysis and workflow development platform; it is a comprehensive, open-source research infrastructure that enables researchers to manage the entire data lifecycle while adhering to the FAIR principles. Developed initially to democratize access to complex bioinformatics analyses and workflows, Galaxy has evolved into a scalable, domain-agnostic platform supporting reproducible research and robust research data management (RDM) across disciplines for two decades. Galaxy offers a user-friendly web interface with thousands of integrated tools and workflows at its core. However, its strength lies in its robust infrastructure, designed for openness, interoperability, and data stewardship. Galaxy supports structured data ingestion, analysis, sharing, publication, and archiving, all within a reproducible and collaborative environment. Galaxy's flexible architecture allows researchers to bring their own compute (BYOC), storage (BYOS), and data (BYOD). It integrates seamlessly with institutional HPC systems, S3-compatible object stores, and platforms like Google Drive, Dropbox, WebDAV, and Nextcloud. Compatible with institutional LIMS and eLab systems, Galaxy enables seamless integration into existing research environments. This supports various use cases, from sensitive data handling and clinical studies to large-scale collaborative projects, while meeting institutional compliance requirements. Galaxy integrates smoothly with research data repositories like Zenodo/InvenioRDM and Dataverse. This enables researchers to publish datasets, workflows, and results with metadata and persistent identifiers, thereby enabling data sharing, long-term preservation, and compliance. This helps make research more transparent, reusable, and trustworthy. Galaxy's BYOC feature allows researchers to perform data analyses on local HPC systems, institutional clusters, or commercial clouds while still using the familiar Galaxy interface and utilizing 1000s of tools and its numerous features. Galaxy's BYOS and BYOD features enable users to directly connect their preferred storage systems, including institutional storage, S3-compatible object stores, or platforms like Nextcloud, Dropbox, and WebDAV, to their analysis environment for seamless data access. Galaxy's European infrastructure (https://usegalaxy.eu) alone serves over 125,000 researchers, making it one of the most widely adopted open science platforms globally. For the NFDI, Galaxy offers a ready-to-integrate component for building and harmonizing discipline-specific RDM workflows, aligning with community-driven standards and metadata models. It lowers technical barriers for researchers while enabling institutions to implement FAIR-by-design data infrastructures. Galaxy supports the export of workflows and analysis results as RO-Crates, ensuring rich, machine-actionable metadata packaging for downstream reuse, preservation, and integration. From real-time collaboration tools to workflow automation and machine learning-ready environments (via integrated Jupyter notebook and RStudio) to publication pipelines, Galaxy bridges the gap between data analysis and sustainable RDM. It gives researchers the tools to do science responsibly, reproducibly, and impactfully. In this session, we will introduce Galaxy as a robust research data management infrastructure that supports researchers and institutions in implementing best practices across the entire data lifecycle. This talk will demonstrate how Galaxy lowers technical barriers, promotes interoperability, and enables researchers to produce FAIR and impactful scientific results across disciplines.

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2025-08-04
DOI
https://doi.org/10.5281/zenodo.16735891
Primary Topic
Research Data Management Practices
Type
article
Field-Weighted Citation Impact
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article

Galaxy a FAIR-by-design platform: Bridging analysis and research data management across disciplines

Zenodo (CERN European Organization for Nuclear Research)
Research Data Management Practices
article

Galaxy a FAIR-by-design platform: Bridging analysis and research data management across disciplines

article en

Abstract

Galaxy [1] is more than a data analysis and workflow development platform; it is a comprehensive, open-source research infrastructure that enables researchers to manage the entire data lifecycle while adhering to the FAIR principles. Developed initially to democratize access to complex bioinformatics analyses and workflows, Galaxy has evolved into a scalable, domain-agnostic platform supporting reproducible research and robust research data management (RDM) across disciplines for two decades. Galaxy offers a user-friendly web interface with thousands of integrated tools and workflows at its core. However, its strength lies in its robust infrastructure, designed for openness, interoperability, and data stewardship. Galaxy supports structured data ingestion, analysis, sharing, publication, and archiving, all within a reproducible and collaborative environment. Galaxy's flexible architecture allows researchers to bring their own compute (BYOC), storage (BYOS), and data (BYOD). It integrates seamlessly with institutional HPC systems, S3-compatible object stores, and platforms like Google Drive, Dropbox, WebDAV, and Nextcloud. Compatible with institutional LIMS and eLab systems, Galaxy enables seamless integration into existing research environments. This supports various use cases, from sensitive data handling and clinical studies to large-scale collaborative projects, while meeting institutional compliance requirements. Galaxy integrates smoothly with research data repositories like Zenodo/InvenioRDM and Dataverse. This enables researchers to publish datasets, workflows, and results with metadata and persistent identifiers, thereby enabling data sharing, long-term preservation, and compliance. This helps make research more transparent, reusable, and trustworthy. Galaxy's BYOC feature allows researchers to perform data analyses on local HPC systems, institutional clusters, or commercial clouds while still using the familiar Galaxy interface and utilizing 1000s of tools and its numerous features. Galaxy's BYOS and BYOD features enable users to directly connect their preferred storage systems, including institutional storage, S3-compatible object stores, or platforms like Nextcloud, Dropbox, and WebDAV, to their analysis environment for seamless data access. Galaxy's European infrastructure (https://usegalaxy.eu) alone serves over 125,000 researchers, making it one of the most widely adopted open science platforms globally. For the NFDI, Galaxy offers a ready-to-integrate component for building and harmonizing discipline-specific RDM workflows, aligning with community-driven standards and metadata models. It lowers technical barriers for researchers while enabling institutions to implement FAIR-by-design data infrastructures. Galaxy supports the export of workflows and analysis results as RO-Crates, ensuring rich, machine-actionable metadata packaging for downstream reuse, preservation, and integration. From real-time collaboration tools to workflow automation and machine learning-ready environments (via integrated Jupyter notebook and RStudio) to publication pipelines, Galaxy bridges the gap between data analysis and sustainable RDM. It gives researchers the tools to do science responsibly, reproducibly, and impactfully. In this session, we will introduce Galaxy as a robust research data management infrastructure that supports researchers and institutions in implementing best practices across the entire data lifecycle. This talk will demonstrate how Galaxy lowers technical barriers, promotes interoperability, and enables researchers to produce FAIR and impactful scientific results across disciplines.

Zenodo (CERN European Organization for Nuclear Research)
University of Freiburg (DE)
Industry, innovation and infrastructure
Openalex Percentile: Top 40%
Research Data Management Practices
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