Research workflows are becoming increasingly complex, often requiring researchers to move data between multiple platforms—from electronic lab notebooks where experiments are documented, to computational platforms where data is analyzed. At the same time, requirements for robust data management and provenance tracking continue to grow. Today, we're excited to announce a step toward eliminating friction by bringing RSpace and Galaxy closer together.

Reducing Manual Data Transfer

RSpace is an open-source research data management platform with an electronic lab notebook and integrated sample management system at its core. It provides researchers across academic institutions worldwide with FAIR data workflows by connecting everyday research tasks with tools, services, and research infrastructure across the entire research data lifecycle.

Galaxy is an open-source workflow platform designed to make computational methods accessible, reusable, and reproducible. Originally developed for computational biology, Galaxy has evolved into a general framework utilized across various scientific disciplines.

Until now, researchers faced a common bottleneck: to analyze data documented in RSpace using Galaxy's computational workflows, they had to manually upload files—a process that introduced potential errors and inefficiencies.

RSpace as an Integrated File Store for Galaxy

Our new integration, implemented through Galaxy pull request #20167, eliminates manual file transfers by making the RSpace Gallery a native file source for Galaxy. The technical foundation rests on RSpace's Python client library, which now provides PyFilesystem2-compatible abstractions for both RSpace's Gallery (the RSpace file store) and Inventory (the sample management system).

Setting up RSpace as a file store in Galaxy is straightforward: researchers authenticate securely with their RSpace API key, configure RSpace as a file source, and then browse and import files directly from their RSpace Gallery without leaving Galaxy. Whether it's microscopy images, sequencing data, or experimental datasets, the data becomes immediately accessible within Galaxy. Additionally, users can write results and workflow provenance back into RSpace for seamless integration into their research documentation and share it with the wider RSpace ecosystem of tools, services, and research infrastructure.

With Galaxy version 25.0 the RSpace file source is available now across the Galaxy project and can be deployed on any Galaxy instance. The integration will be available on the European Galaxy instance (https://usegalaxy.eu/) as soon as the latest version has been deployed. Research organizations interested in implementing this integration can find detailed technical documentation in the Galaxy file source implementation update and on the RSpace documentation.

What's Coming Next

Similar file access capabilities for RSpace's sample management system and the planned Workspace filesystem will be available as Galaxy file sources in the future. This will allow researchers to access files attached to specific documents and samples—maintaining crucial links between physical samples and their associated data throughout the analysis process.

This integration represents the first phase of a broader collaboration. We're developing solutions that will allow researchers to execute Galaxy workflows directly from within RSpace. Soon, a researcher who has documented e.g. an RNA-seq experiment in RSpace will be able to select relevant files in their electronic notebook and launch standard analysis workflows with minimal setup, making computational analysis accessible to researchers regardless of their familiarity with Galaxy's interface.

A Step Toward FAIR-Enabling Research Infrastructure

By creating seamless connections between research documentation and computational analysis platforms, we're helping researchers focus on their science rather than data transfer logistics. Through connectivity with research resources, RSpace can act as a value-adding bridge between active research and the planning, archiving, and storage phases of the research lifecycle, facilitating streamlined data and metadata flow while enhancing FAIRness. This integration represents therefore more than a technical improvement—it's a step toward research infrastructure that truly serves science, where tools work together to enhance FAIRness and accelerate the pace of discovery.

This integration was developed through collaboration between Research Space and the Galaxy Europe team at the University of Freiburg. Technical implementation was led by José Manuel Domínguez at the University of Freiburg, building on RSpace's enhanced Python client capabilities developed by Robert Lamacraft.

To learn more about RSpace and Galaxy, visit researchspace.com and galaxyproject.org.

‍