From 0c25f2a51d284de0037066de623bee487772a8b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 11 Mar 2026 13:56:17 +0100 Subject: [PATCH 01/19] add findability --- content/fair/findability/index.md | 149 ++++++++++++++++++++++++++++++ 1 file changed, 149 insertions(+) create mode 100644 content/fair/findability/index.md diff --git a/content/fair/findability/index.md b/content/fair/findability/index.md new file mode 100644 index 0000000000..c25c431187 --- /dev/null +++ b/content/fair/findability/index.md @@ -0,0 +1,149 @@ +--- +title: Galaxy and Findability +highlight: true +--- + +Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. + +
ELIXIR RIR logo
+
+ +Galaxy is an open-source platform for scientific data analysis and sharing. It operationalises the FAIR “F” principle (Findability) through a combination of technical, organisational, and community-driven measures. These ensure that tools, workflows, datasets, and other research objects are easy to find and access by users and machines. +This page highlights Galaxy’s findability mechanisms, their alignment with Research Data Management (RDM) principles, and their integration with interoperability frameworks such as those promoted by ELIXIR, GA4GH, and EOSC. + +# Resource Facilitation for Scientific Research + +## Galaxy as a Findable Research Platform + +Galaxy is designed to make scientific data analysis transparent, reproducible, and reusable. By embedding findability into its core architecture, Galaxy ensures that research objects — including tools, workflows, datasets, electronic lab books, results, and visualisations — are identifiable, described, and programmatically accessible. This approach supports researchers in locating, citing, and reusing resources, while capturing all provenance information for full traceability. + +Galaxy’s findability features are very useful for non-technical users. They can use search interfaces, structured metadata, and integration with external registries. The platform follows community standards (e.g., EDAM ontology, GA4GH DRS, RO-Crate) and contributes actively to upstream projects like WorkflowHub, Dockstore, bio.tools, Research Software Ecosystem and ELIXIR registries. + +# Scope and User Base + +Galaxy’s findability mechanisms serve a diverse and global user base across the usegalaxy. instances* (US, EU, AU), which collectively support tens of thousands of registered users. These users come from multiple scientific domains, such as omics and climate science and include researchers, educators and data stewards. Many users lack a background in data-intensive methodologies but rely on Galaxy to develop, share, and execute workflows at scale. + +To support this community, Galaxy provides: + +- Persistent and unique identifiers for all research objects. +- Structured and machine-readable metadata for tools, workflows, and datasets. +- Versioning and provenance tracking to ensure temporal traceability. +- Programmatic access via a comprehensive API, enabling integration with external portals and services. + +Galaxy’s findability features are further improved by initiatives such as the Galaxy Training Network (GTN), which offers training materials to help users leverage the platform’s discovery capabilities. + + +# Persistent and Unique Identifiers +## Multi-Level Identifier Assignment + +Galaxy implements persistent and unique identifiers at every level of its architecture, ensuring traceability, reproducibility, and citation readiness: + +| Object Type | Identifier Mechanism | Purpose | +|-------------------|-------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------| +| Tools | Stable, versioned tool IDs | Enable precise tool citation and version tracking. | +| Workflows | Resolvable identifiers via WorkflowHub, Dockstore, and internal Galaxy IDs | Support workflow sharing, discovery, and reuse. | +| Datasets | GA4GH DRS identifiers for externally stored data; internal Galaxy dataset IDs | Facilitate dataset referencing and interoperability with external systems. | +| Histories, Jobs | Unique internal Galaxy IDs | Ensure traceability of all analysis steps and outputs. | + +These identifier mechanisms are aligned with RDM best practices and enable Galaxy to function as a FAIR-compliant research infrastructure. + +# Rich and Structured Metadata +## Metadata as the Backbone of Findability + +Galaxy enforces the use of structured standardised metadata to enhance the discoverability of research objects by both humans and machines: + +- Tools: + - Annotated with the EDAM ontology for semantic grouping and domain-specific discovery. + - Metadata includes version, parameters, dependencies, citations, and container information. +- Workflows: + - Descriptive metadata (title, abstract, creator, tags) and version histories. + - Versioning allows users to discover and reference specific revisions. +- Datasets: + - Strongly typed datatypes ensure compatibility with tools accepting specific formats. + - Dataset collections act as structured, queryable entities. +- Provenance: + - Records connect datasets to the exact workflow and tool configuration used to generate them. + - Metadata in Galaxy is not only stored but also machine-retrievable via the Galaxy API, ensuring compliance with machine-actionable FAIR requirements. + +# Search and Discovery Mechanisms +## Multi-Layered Discovery + +Galaxy provides multiple layers of discovery to cater to diverse user needs, ensuring that tools, workflows, and datasets are easily accessible — whether through intuitive interfaces, structured metadata, or integration with external registries. + +**User Interface** +- Simple and advanced search within the Galaxy interface. +- Ontology-based grouping of tools (e.g., via EDAM). + +**Extensive Tool Search Capabilities** +Galaxy offers advanced search functionalities to help users to quickly locate the tools they need. Users can: +- Search by datatype: Find tools compatible with specific data formats (e.g., FASTQ, BAM, NetCDF), ensuring integration into workflows. +- Search in help texts and documentation: Locate tools based on keywords in their descriptions, parameters, or help sections, making it easier to discover domain-specific functionalities. +- Explore tools from training materials: Directly access tools used in Galaxy Training Network (GTN) tutorials, enabling users to replicate analyses from educational resources or discover best-practice workflows. +- Link to relevant training: From tool pages or search results, users can navigate to GTN training materials that demonstrate tool usage, fostering both discovery and skill development. + +**External Registries:** +- Tool distribution via the Galaxy ToolShed (“AppStore” model). +- Public workflows are discoverable through WorkflowHub and curated by the Intergalactic Workflow Commission (IWC). + +**Interoperability Catalogues:** +- Registration of Galaxy resources in ELIXIR registries, Sextant, and other global discovery infrastructures. + +These mechanisms — from search interfaces to tool discovery and integration with global registries — ensure that Galaxy’s research assets remain findable, reusable, and accessible across institutional, disciplinary, and geographic boundaries. By combining technical infrastructure, structured metadata, and educational resources, Galaxy empowers users to locate and leverage the tools and workflows they need for their research. + +# Programmatic Findability and API Access +## API-Driven Discovery + +Galaxy’s comprehensive API enables programmatic discovery of tools, workflows, and datasets, supporting: +- Machine-readable access to structured metadata. +- Integration with external portals and services (e.g., EOSC, ELIXIR). +- Automated harvesting and federation of research objects. +This API-driven design ensures that Galaxy resources are fully discoverable within interoperable digital research ecosystems, aligning with the platform’s role as a Recommended Interoperability Resource (RIR) for ELIXIR. + +# Research Data Management Perspective +## Findability as an RDM Principle + +From an RDM standpoint, Galaxy embeds findability into the lifecycle of computational research: +- Persistent identifiers enable citation, tracking, and long-term accessibility. +- Structured metadata supports machine indexing and semantic discoverability. +- Versioning ensures traceable evolution of analyses. +- API access enables automated harvesting and federation with other platforms. + +Galaxy’s approach to findability is not an afterthought but a core architectural principle, operationalised through: +- Integration with community standards (e.g., EDAM, GA4GH DRS, RO-Crate). +- Collaboration with ELIXIR, EOSC, and other interoperability initiatives. +- Active contribution to upstream projects (e.g., WorkflowHub, Dockstore). + +# Conclusion: Findability as a Pillar of FAIR Research +Galaxy’s implementation of findability is holistic, integrating infrastructure, community standards, and interoperability frameworks. By ensuring that research objects are persistently identifiable, richly described, and programmatically accessible, Galaxy empowers researchers to conduct FAIR-compliant, reproducible, and collaborative science. + +# Legal framework, funding, and governance + +## Legal framework + +Galaxy is available under a small range of licenses: +* Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) +* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License +* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt +* Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. + +## Privacy/Ethics policy + +The Galaxy framework has a GDPR configuration option, which will make sure that a deployed instance is GDPR-compliant (to the best of our knowledge). This option is enabled at the European Galaxy server (and related resources). Please read more about it at: +https://usegalaxy-eu.github.io/gdpr/ +and +https://docs.galaxyproject.org/en/master/admin/special_topics/gdpr_compliance.html + +Notably, the Galaxy Community is dedicated to provide a harassment-free experience for everyone, thus living a [Code of Conduct](https://galaxyproject.org/community/coc/), outlining the behaviours deemed acceptable and unacceptable. + +## Funding & sustainability plan + +The Galaxy Project is embedded in national and international funding streams. Notably, these include NIH and NSF (US), ELIXIR, EOSC and BMBF (EU), Bioplatforms and Research Data Commons (AUS). More information on the continental usegalaxy.* instances you find on the bottom of the Galaxy Hub pages, and e.g. [here](https://usegalaxy-eu.github.io/freiburg/projects). However, the Galaxy project is built by many contributors from all over the world, so that the underlying funding is much more diverse and is subject to constant change in detail. This global community is well connected and capable of bridging funding gaps and re-allocating resources by strong vice-versa support. + +## Governance + +Please read more about the Galaxy governance at: https://galaxyproject.org/community/governance +and +https://docs.galaxyproject.org/en/master/project/organization.html (code governance). + +The ELIXIR Galaxy Community is the European part of the Galaxy community, similar to the Biocommons in Australia. Scientific communities, national and international communities are coming together to govern the Galaxy project as part of working groups or the steering committee. From 96c006f7575fb410839b8149368a851cb089dfdb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 11 Mar 2026 14:20:04 +0100 Subject: [PATCH 02/19] add reusability --- content/fair/reusability/index.md | 118 ++++++++++++++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 content/fair/reusability/index.md diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md new file mode 100644 index 0000000000..f06384ae0f --- /dev/null +++ b/content/fair/reusability/index.md @@ -0,0 +1,118 @@ +--- +title: Galaxy and Reusability +highlight: true +--- + +Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. + +
ELIXIR RIR logo
+
+ +Galaxy operationalises the FAIR “R” principle (Reusability) by providing technical, organisational, and community-driven mechanisms that ensure research objects, such as tools, workflows, histories, and visualisations, can be shared, reproduced, and adapted across diverse scientific contexts. Reusability in Galaxy is about preserving provenance, resolving dependencies, and enabling long-term reproducibility, all while adhering to open standards and best practices in Research Data Management (RDM). +Galaxy’s architecture relies on container technologies, provenance tracking, and community-driven quality assurance frameworks. This architecture fosters a culture of reusable, high-quality, and sustainable research. + +# Resource Facilitation for Reusable Research +## Galaxy as a Platform for Reproducible Science + +Galaxy is designed to lower the barriers to reproducible and reusable data analysis. By capturing the full context of computational research, Galaxy ensures that analyses can be rerun, shared, and adapted with minimal difficulties. This is achieved through: +- Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. +- Tight integration with Biocontainers, ensuring that tools and workflows are portable and executable across different infrastructures. +- Comprehensive provenance tracking, which records every parameter, input, tool version, and container used in an analysis. + +All of this makes Galaxy a trusted platform for researchers who need to ensure that their work is ready for reuse by others. + +# Scope and User Base +Galaxy’s reusability features serve a global, multidisciplinary community of researchers, educators, and data stewards. The platform’s usegalaxy. instances* (US, EU, AU) support tens of thousands of users, many of whom rely on Galaxy to develop, share, and reuse workflows and datasets in scientific domains going from genomics to climate science. + +## Capturing and Leveraging Provenance: the backbone of reusability + +Galaxy automatically captures comprehensive provenance for every analysis, including: +- Tool versions, parameters, and inputs. +- Container or environment used. +- Exact workflow steps and intermediate datasets. + +Key user needs addressed by Galaxy’s reusability features include: +- Sharing analyses with collaborators or the broader scientific community. +- Reproducing results for validation, publication, or further analysis. +- Adapting existing workflows to new datasets or research questions. +- Ensuring long-term accessibility of research objects through standardised exports and imports. + +To support these needs, the provenance in Galaxy is actionable and provides: +- Sharing permissions for histories, datasets, visualisations, and workflows (e.g., with specific users or globally). +- Reproducibility, enabling users to rerun tools or workflows at any point in their analysis even after a failure. +- Avoiding redundant computations as provenance data powers Galaxy job cache +- Standardised export formats (e.g., RO-Crate, BioComputeObjects) for long-term archiving, sharing, and reuse. + +## Export and Import for Long-Term Reuse + +Galaxy supports the export and import of entire histories, workflows, and datasets, enabling: +- Archiving in repositories like Zenodo. +- Sharing with collaborators or the public. +- Importing into Galaxy for further analysis or adaptation. + +For example, a history exported as an RO-Crate can be imported into Galaxy years later, preserving all metadata, provenance, and data relationships. + +# Dependency Resolution and Containerisation +## Ensuring Portability and Reproducibility + +Galaxy resolves dependencies and ensures reproducibility through containerisation and environment management: + +| Technology | Role in Galaxy | Benefit for Reusability | +|---------------|-----------------------------------------------------------------|--------------------------------------------------------------------------| +| Conda | Manages tool dependencies and environments. | Ensures tools run consistently across different Galaxy instances. | +| Docker | Supports containerised tool execution. | Enables portability and isolation of tool environments. | +| Singularity | Provides secure, reproducible containers for HPC environments. | Facilitates reuse in high-performance computing contexts. | +| Biocontainers | Pre-built, standardised containers for bioinformatics tools. | Ensures compatibility and reduces setup overhead for users. | + + +Galaxy’s integration with Biocontainers is particularly significant, as it allows users to leverage many, community-curated repositories of containerised tools, reducing the manual dependency resolution and enhancing the portability of workflows. + +# Quality Assurance and Testing Frameworks +## Ensuring Long-Term Reusability + +Galaxy’s commitment to reusability extends to quality assurance and testing frameworks, which ensure that tools and workflows remain functional and reliable over time: + +| Framework/Initiative | Role | Impact on Reusability | +|-----------------------------------------|------------------------------------------------------------------------|-------------------------------------------------------------------------------------| +| Intergalactic Workflow Commission (IWC) | Curates and tests high-quality, reusable workflows. | Provides a catalogue of trusted, well-documented workflows for the community. | +| Planemo | CLI tool for developing, testing, and sharing Galaxy tools/workflows. | Enables developers to validate and package tools/workflows for reuse. | +| Galaxy Training Network (GTN) | Develops interactive training materials on workflow reuse and sharing. | Educates users on best practices for creating and reusing Galaxy resources. | + + +These frameworks ensure that Galaxy’s tools and workflows are reusable and reliable, which reduces the risk of errors and enhances trust in shared resources. + +# Conclusion: Reusability as a Cornerstone of Open Science + +Galaxy’s approach to reusability is comprehensive, integrating technical infrastructure, community standards, and quality assurance frameworks. Indeed, from each analysis a workflow can be extracted in standard formats. This workflow can be registered in WorkflowHub or Similar registries. Later, a workflow file can be imported to Galaxy to reproduce the same analysis or perform a similar analysis. This empowers researchers to build on each other’s work, accelerating scientific discovery and innovation. + +# Legal framework, funding, and governance + +## Legal framework + +Galaxy is available under a small range of licenses: +* Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) +* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License +* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt +* Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. + +## Privacy/Ethics policy + +The Galaxy framework has a GDPR configuration option, which will make sure that a deployed instance is GDPR-compliant (to the best of our knowledge). This option is enabled at the European Galaxy server (and related resources). Please read more about it at: +https://usegalaxy-eu.github.io/gdpr/ +and +https://docs.galaxyproject.org/en/master/admin/special_topics/gdpr_compliance.html + +Notably, the Galaxy Community is dedicated to provide a harassment-free experience for everyone, thus living a [Code of Conduct](https://galaxyproject.org/community/coc/), outlining the behaviours deemed acceptable and unacceptable. + +## Funding & sustainability plan + +The Galaxy Project is embedded in national and international funding streams. Notably, these include NIH and NSF (US), ELIXIR, EOSC and BMBF (EU), Bioplatforms and Research Data Commons (AUS). More information on the continental usegalaxy.* instances you find on the bottom of the Galaxy Hub pages, and e.g. [here](https://usegalaxy-eu.github.io/freiburg/projects). However, the Galaxy project is built by many contributors from all over the world, so that the underlying funding is much more diverse and is subject to constant change in detail. This global community is well connected and capable of bridging funding gaps and re-allocating resources by strong vice-versa support. + +## Governance + +Please read more about the Galaxy governance at: https://galaxyproject.org/community/governance +and +https://docs.galaxyproject.org/en/master/project/organization.html (code governance). + +The ELIXIR Galaxy Community is the European part of the Galaxy community, similar to the Biocommons in Australia. Scientific communities, national and international communities are coming together to govern the Galaxy project as part of working groups or the steering committee. From ffcd586d95610b17ab2a0bcb3fd5e2dcf8294112 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Wed, 11 Mar 2026 14:57:25 +0100 Subject: [PATCH 03/19] add accessibility --- content/fair/accessibility/index.md | 142 ++++++++++++++++++++++++++++ 1 file changed, 142 insertions(+) create mode 100644 content/fair/accessibility/index.md diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md new file mode 100644 index 0000000000..282ac0352c --- /dev/null +++ b/content/fair/accessibility/index.md @@ -0,0 +1,142 @@ +--- +title: Galaxy and Accessibility +highlight: true +--- + +Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. + +
ELIXIR RIR logo
+
+ +Galaxy embodies the FAIR “A” principle (Accessibility) by providing an open, inclusive, and technically robust platform that ensures research tools, workflows, and data are available, usable, and adaptable to a diverse global user base. Accessibility in Galaxy is not limited to technical access, it encompasses open-source design, flexible authentication, multi-modal interfaces, distributed computing, and data integration with standard repositories and cloud infrastructures. +Galaxy’s architecture is based on community-driven initiatives and integration with global standards and services. This page highlights how this architecture allows to lower barriers to entry for researchers, educators, and data stewards, regardless of their technical expertise or institutional affiliation. + +# Resource Facilitation for Accessible Research +## Galaxy as an Open and Adaptable Platform + +Galaxy is designed to be accessible by default, offering multiple entry points and interfaces to accommodate users with varying levels of technical skill. The platform’s open-source nature ensures transparency, customisability, and community-driven innovation. Its architecture allows for deployment in diverse contexts, from public servers to private, and institution-specific instances. +Key features enabling accessibility include: +- Open-source design: Galaxy’s codebase is publicly available (https://github.com/galaxyproject), allowing anyone to deploy, modify, or extend the platform. +- Subdomains and Labs: Galaxy supports community-specific subdomains (e.g., for genomics, earth system science, or ecology) and Galaxy Labs for specialised scientific fields. +- Multi-lingual and multi-interface support: Users can interact with Galaxy via web interfaces, APIs, or interactive environments (e.g., RStudio, Jupyter). + +# Scope and User Base + +Galaxy’s accessibility features serve a global, multidisciplinary community of researchers, educators, and data managers. The platform’s public instances (e.g., usegalaxy.eu, usegalaxy.org, usegalaxy.org.au) collectively support tens of thousands of users, including: +- Researchers with limited technical expertise, who rely on Galaxy’s intuitive interfaces. +- Data scientists, who leverage Galaxy’s distributed computing and API-driven automation. +- Educators and trainees, who use Galaxy’s training materials (e.g., via the Galaxy Training Network, GTN) to onboard new users. + +Galaxy’s accessibility is further enhanced by its integration with federated identity providers, ensuring secure and easy access for users worldwide. + +# Data Accessibility: Connecting to Global Repositories +## Flexible Data Sources and Destinations + +Galaxy provides comprehensive support for accessing and exporting data from/to a wide range of standard repositories and cloud storage solutions. This ensures that users can retrieve, analyse, and share data without being constrained by local storage or institutional silos. + +**Data Retrieval: Supported Protocols and Repositories** + +Galaxy’s file-sources and object stores enable access to: +- Standard data repositories: + - Zenodo, Invenio, Dataverse, Nextcloud, OpenCloud. + - S3, FTP, WebDAV, iRODS, OneData. + All available repositories are findable here https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/files/sources + +- Domain-specific repositories (via API): + - Copernicus (climate/earth observation), ENA (nucleotides), NCBI, UniProt, Ensembl, BioMart, AquaINFRA (aquatic sciences). + +**Data Export: Sharing and Archiving** + +Users can export data to: +- Standard repositories (e.g., ENA for nucleotide sequences). +- Writable file sources (e.g., FTP, S3, WebDAV). + +**Object Stores: Scalable and User-Owned Storage** + +Galaxy’s object stores allow for flexible storage solutions: +- Institution-funded storage (e.g., de.NBI-cloud for European users). +- User-owned storage (e.g., AWS, GCS, S3, iRODS), which can be integrated into Galaxy instances. + +# Tool Accessibility: Usable, Annotated, and Validated +## A Rich Ecosystem of Accessible Tools + +Galaxy hosts thousands of tools, each designed to be accessible, documented, and easy to use: +- Graphical and programmatic access: tools can be accessed via Galaxy’s web interface or API, supporting both manual and automated workflows. +- Interactive environments: users can launch RStudio, Jupyter, and other interactive tools directly within Galaxy. +- Extensive annotations: tools are enriched with metadata, including: + - EDAM ontology for semantic categorisation. + - DOIs for citation and traceability. + - Dedicated help sections and parameter validation to prevent user errors. + +## Authentication and Security: Federated and Flexible + +Galaxy supports diverse authentication methods to ensure secure and inclusive access: +- Public account creation: Anyone can create an account on public Galaxy servers using simple username/password or federated identity providers (e.g., EGI Check-in, AAI). +- Federated identity management: Galaxy’s authentication subsystem supports LDAP, PAM, OIDC, and other protocols, enabling integration with institutional or national identity providers. + +# Programmatic Accessibility: APIs and Distributed Computing +## OpenAPI-Based Integration + +Galaxy’s comprehensive API (based on the OpenAPI standard) enables programmatic access to all platform features, supporting: +- Automation of workflows and data analysis. +- Integration with external portals, services, and scripts. +- Custom interfaces: The API powers Galaxy’s web interface and can be used to build alternative frontends or specialised tools. + +## Distributed Computing with Pulsar + +Galaxy’s use of Pulsar, a lightweight distributed computing system, extends its accessibility by: +- Enabling workflows to run on remote resources, including HPC clusters and cloud infrastructures. +- Supporting scalable, high-performance computing for resource-intensive analyses. + +# Community Support and Training +## Onboarding and Help Channels + +Galaxy’s accessibility is reinforced by community support and training resources: +- Galaxy Training Network (GTN): provides interactive tutorials and FAIR training materials to help users get started. +- Help channels: users can access support via: + - Matrix chat (e.g., #galaxyproject:matrix.org). + - Help boards (e.g., help.galaxyproject.org). + - Dedicated documentation and video tutorials. + +## Outreach and Inclusivity + +Galaxy’s global community actively promotes accessibility through: +- Multilingual resources and localised instances. +- Outreach events and workshops to onboard new users. +- Collaborations with initiatives like ELIXIR, EOSC, and national networks to ensure Galaxy remains open and inclusive. + +# Conclusion: Accessibility as a Catalyst for Open Science + +Galaxy’s commitment to accessibility ensures that researchers of all backgrounds can discover, use, and contribute to the platform’s rich ecosystem of tools, workflows, and data. By combining open-source design, flexible authentication, distributed computing, and community support, Galaxy lowers the barriers to FAIR, reproducible, and collaborative science. + +# Legal framework, funding, and governance + +## Legal framework + +Galaxy is available under a small range of licenses: +* Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) +* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License +* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt +* Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. + +## Privacy/Ethics policy + +The Galaxy framework has a GDPR configuration option, which will make sure that a deployed instance is GDPR-compliant (to the best of our knowledge). This option is enabled at the European Galaxy server (and related resources). Please read more about it at: +https://usegalaxy-eu.github.io/gdpr/ +and +https://docs.galaxyproject.org/en/master/admin/special_topics/gdpr_compliance.html + +Notably, the Galaxy Community is dedicated to provide a harassment-free experience for everyone, thus living a [Code of Conduct](https://galaxyproject.org/community/coc/), outlining the behaviours deemed acceptable and unacceptable. + +## Funding & sustainability plan + +The Galaxy Project is embedded in national and international funding streams. Notably, these include NIH and NSF (US), ELIXIR, EOSC and BMBF (EU), Bioplatforms and Research Data Commons (AUS). More information on the continental usegalaxy.* instances you find on the bottom of the Galaxy Hub pages, and e.g. [here](https://usegalaxy-eu.github.io/freiburg/projects). However, the Galaxy project is built by many contributors from all over the world, so that the underlying funding is much more diverse and is subject to constant change in detail. This global community is well connected and capable of bridging funding gaps and re-allocating resources by strong vice-versa support. + +## Governance + +Please read more about the Galaxy governance at: https://galaxyproject.org/community/governance +and +https://docs.galaxyproject.org/en/master/project/organization.html (code governance). + +The ELIXIR Galaxy Community is the European part of the Galaxy community, similar to the Biocommons in Australia. Scientific communities, national and international communities are coming together to govern the Galaxy project as part of working groups or the steering committee. From bfe3bbed8538decaf2edc9aa879d44adac1bd840 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:21:57 +0100 Subject: [PATCH 04/19] add Armin notes --- content/fair/accessibility/index.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index 282ac0352c..4c0148eae4 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -23,9 +23,9 @@ Key features enabling accessibility include: # Scope and User Base Galaxy’s accessibility features serve a global, multidisciplinary community of researchers, educators, and data managers. The platform’s public instances (e.g., usegalaxy.eu, usegalaxy.org, usegalaxy.org.au) collectively support tens of thousands of users, including: -- Researchers with limited technical expertise, who rely on Galaxy’s intuitive interfaces. +- Researchers with limited computational expertise, who rely on Galaxy’s intuitive interfaces. - Data scientists, who leverage Galaxy’s distributed computing and API-driven automation. -- Educators and trainees, who use Galaxy’s training materials (e.g., via the Galaxy Training Network, GTN) to onboard new users. +- Educators and trainees, who use Galaxy’s training materials (e.g., via the Galaxy Training Network (GTN)) to onboard new users. Galaxy’s accessibility is further enhanced by its integration with federated identity providers, ensuring secure and easy access for users worldwide. @@ -40,7 +40,7 @@ Galaxy’s file-sources and object stores enable access to: - Standard data repositories: - Zenodo, Invenio, Dataverse, Nextcloud, OpenCloud. - S3, FTP, WebDAV, iRODS, OneData. - All available repositories are findable here https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/files/sources + All available repositories are findable here: https://training.galaxyproject.org/training-material/faqs/galaxy/manage_your_repositories.html - Domain-specific repositories (via API): - Copernicus (climate/earth observation), ENA (nucleotides), NCBI, UniProt, Ensembl, BioMart, AquaINFRA (aquatic sciences). @@ -71,7 +71,7 @@ Galaxy hosts thousands of tools, each designed to be accessible, documented, and ## Authentication and Security: Federated and Flexible Galaxy supports diverse authentication methods to ensure secure and inclusive access: -- Public account creation: Anyone can create an account on public Galaxy servers using simple username/password or federated identity providers (e.g., EGI Check-in, AAI). +- Public account creation: Anyone can create an account on public Galaxy servers using simple username/password or federated identity providers (e.g., EGI Check-in, EOSC AAI, and LS login). - Federated identity management: Galaxy’s authentication subsystem supports LDAP, PAM, OIDC, and other protocols, enabling integration with institutional or national identity providers. # Programmatic Accessibility: APIs and Distributed Computing @@ -84,7 +84,7 @@ Galaxy’s comprehensive API (based on the OpenAPI standard) enables programmati ## Distributed Computing with Pulsar -Galaxy’s use of Pulsar, a lightweight distributed computing system, extends its accessibility by: +Galaxy’s use of Pulsar, a lightweight distributed job execution application, extends its accessibility by: - Enabling workflows to run on remote resources, including HPC clusters and cloud infrastructures. - Supporting scalable, high-performance computing for resource-intensive analyses. @@ -107,7 +107,7 @@ Galaxy’s global community actively promotes accessibility through: # Conclusion: Accessibility as a Catalyst for Open Science -Galaxy’s commitment to accessibility ensures that researchers of all backgrounds can discover, use, and contribute to the platform’s rich ecosystem of tools, workflows, and data. By combining open-source design, flexible authentication, distributed computing, and community support, Galaxy lowers the barriers to FAIR, reproducible, and collaborative science. +Galaxy’s commitment to accessibility ensures that researchers of all backgrounds can discover, use, and contribute to the platform’s rich ecosystem of tools, workflows, and data. By combining open-source design, flexible authorisation and authentication, distributed computing, and community support, Galaxy lowers the barriers to FAIR, reproducible, and collaborative science. # Legal framework, funding, and governance From b976987aa8b687a25c5d08a251ce26c6139db1b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:22:50 +0100 Subject: [PATCH 05/19] fix typo --- content/fair/reusability/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index f06384ae0f..74beca2c56 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -22,7 +22,7 @@ Galaxy is designed to lower the barriers to reproducible and reusable data analy All of this makes Galaxy a trusted platform for researchers who need to ensure that their work is ready for reuse by others. # Scope and User Base -Galaxy’s reusability features serve a global, multidisciplinary community of researchers, educators, and data stewards. The platform’s usegalaxy. instances* (US, EU, AU) support tens of thousands of users, many of whom rely on Galaxy to develop, share, and reuse workflows and datasets in scientific domains going from genomics to climate science. +Galaxy’s reusability features serve a global, multidisciplinary community of researchers, educators, and data stewards. The platform’s usegalaxy.* instances (US, EU, AU) support tens of thousands of users, many of whom rely on Galaxy to develop, share, and reuse workflows and datasets in scientific domains going from genomics to climate science. ## Capturing and Leveraging Provenance: the backbone of reusability From 3d62e8279ac34f40659a6966b5dd8a8b7e49b19d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:23:52 +0100 Subject: [PATCH 06/19] fix typo --- content/fair/findability/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/fair/findability/index.md b/content/fair/findability/index.md index c25c431187..5576616a43 100644 --- a/content/fair/findability/index.md +++ b/content/fair/findability/index.md @@ -21,7 +21,7 @@ Galaxy’s findability features are very useful for non-technical users. They c # Scope and User Base -Galaxy’s findability mechanisms serve a diverse and global user base across the usegalaxy. instances* (US, EU, AU), which collectively support tens of thousands of registered users. These users come from multiple scientific domains, such as omics and climate science and include researchers, educators and data stewards. Many users lack a background in data-intensive methodologies but rely on Galaxy to develop, share, and execute workflows at scale. +Galaxy’s findability mechanisms serve a diverse and global user base across the usegalaxy.* instances (US, EU, AU), which collectively support tens of thousands of registered users. These users come from multiple scientific domains, such as omics and climate science and include researchers, educators and data stewards. Many users lack a background in data-intensive methodologies but rely on Galaxy to develop, share, and execute workflows at scale. To support this community, Galaxy provides: From 57cd21fad45baaf0022c41bd9f86ba5ffdeab1aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:28:23 +0100 Subject: [PATCH 07/19] add paper reference --- content/fair/reusability/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index 74beca2c56..c5e85b94b6 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -14,7 +14,7 @@ Galaxy’s architecture relies on container technologies, provenance tracking, a # Resource Facilitation for Reusable Research ## Galaxy as a Platform for Reproducible Science -Galaxy is designed to lower the barriers to reproducible and reusable data analysis. By capturing the full context of computational research, Galaxy ensures that analyses can be rerun, shared, and adapted with minimal difficulties. This is achieved through: +Galaxy is designed to lower the barriers to reproducible and reusable data analysis as described in the paper [Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014) . By capturing the full context of computational research, Galaxy ensures that analyses can be rerun, shared, and adapted with minimal difficulties. This is achieved through: - Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. - Tight integration with Biocontainers, ensuring that tools and workflows are portable and executable across different infrastructures. - Comprehensive provenance tracking, which records every parameter, input, tool version, and container used in an analysis. From bc501b862ba0ba67c7612f73643c5aa4e1aa2ea0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:30:04 +0100 Subject: [PATCH 08/19] adapt bullet point avoid repetition --- content/fair/reusability/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index c5e85b94b6..d6f3e284ea 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -15,8 +15,7 @@ Galaxy’s architecture relies on container technologies, provenance tracking, a ## Galaxy as a Platform for Reproducible Science Galaxy is designed to lower the barriers to reproducible and reusable data analysis as described in the paper [Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014) . By capturing the full context of computational research, Galaxy ensures that analyses can be rerun, shared, and adapted with minimal difficulties. This is achieved through: -- Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. -- Tight integration with Biocontainers, ensuring that tools and workflows are portable and executable across different infrastructures. +- Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. Indeeed, the tight integration with Biocontainers, for example, ensures that tools and workflows are portable and executable across different infrastructures. - Comprehensive provenance tracking, which records every parameter, input, tool version, and container used in an analysis. All of this makes Galaxy a trusted platform for researchers who need to ensure that their work is ready for reuse by others. From a0f552cfe71f5d3758da9dbd094f222c9f12d678 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:30:22 +0100 Subject: [PATCH 09/19] fix typo --- content/fair/reusability/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index d6f3e284ea..c4d609a39c 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -15,7 +15,7 @@ Galaxy’s architecture relies on container technologies, provenance tracking, a ## Galaxy as a Platform for Reproducible Science Galaxy is designed to lower the barriers to reproducible and reusable data analysis as described in the paper [Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014) . By capturing the full context of computational research, Galaxy ensures that analyses can be rerun, shared, and adapted with minimal difficulties. This is achieved through: -- Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. Indeeed, the tight integration with Biocontainers, for example, ensures that tools and workflows are portable and executable across different infrastructures. +- Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. Indeed, the tight integration with Biocontainers, for example, ensures that tools and workflows are portable and executable across different infrastructures. - Comprehensive provenance tracking, which records every parameter, input, tool version, and container used in an analysis. All of this makes Galaxy a trusted platform for researchers who need to ensure that their work is ready for reuse by others. From 653b7f299e61e4fda452e6d6ac1ac89ff68ebe62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 09:40:22 +0100 Subject: [PATCH 10/19] add tool versions and re-run button --- content/fair/reusability/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index c4d609a39c..3a028b3a3e 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -17,6 +17,8 @@ Galaxy’s architecture relies on container technologies, provenance tracking, a Galaxy is designed to lower the barriers to reproducible and reusable data analysis as described in the paper [Practical Computational Reproducibility in the Life Sciences](https://doi.org/10.1016/j.cels.2018.03.014) . By capturing the full context of computational research, Galaxy ensures that analyses can be rerun, shared, and adapted with minimal difficulties. This is achieved through: - Dependency resolution via containerisation with technologies such as Conda, Docker, Singularity. Indeed, the tight integration with Biocontainers, for example, ensures that tools and workflows are portable and executable across different infrastructures. - Comprehensive provenance tracking, which records every parameter, input, tool version, and container used in an analysis. +- Long-term access to tool versions: Galaxy preserves all versions of tools, which ensures that even older versions remain accessible to users years after their release. This guarantees that old analyses can always be reproduced exactly as they were originally designed. +- Easy re-execution of tools: users can rerun tools and workflows with a single click using the reload button, even for analyses done months or years earlier. This feature with the preserved tool versions and complete provenance records ones, makes Galaxy a robust platform for long-term reproducibility. All of this makes Galaxy a trusted platform for researchers who need to ensure that their work is ready for reuse by others. From f49a1a1eb3a84b35fcb4b026419256d2ac257e28 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:20:49 +0100 Subject: [PATCH 11/19] Change License details --- content/fair/reusability/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index 3a028b3a3e..5eb73e1b19 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -92,8 +92,7 @@ Galaxy’s approach to reusability is comprehensive, integrating technical infra Galaxy is available under a small range of licenses: * Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* The [codebase](https://github.com/galaxyproject/galaxy) is licensed under the MIT License * Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt * Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. From 803cbc432b318b767070e0cc711bc44ed073463c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:21:33 +0100 Subject: [PATCH 12/19] Update index.md --- content/fair/interoperability/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/content/fair/interoperability/index.md b/content/fair/interoperability/index.md index b93540f5c7..315b7d7599 100644 --- a/content/fair/interoperability/index.md +++ b/content/fair/interoperability/index.md @@ -115,8 +115,7 @@ In terms of tutorials and training, videos (screen casts) are available on Youtu Galaxy is available under a small range of licenses: * Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* The [codebase](https://github.com/galaxyproject/galaxy) is licensed under the MIT License * Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt * Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. From 78638cf874ceeacadeeb4d84b0ef4fa6aebef951 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:21:57 +0100 Subject: [PATCH 13/19] license --- content/fair/findability/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/content/fair/findability/index.md b/content/fair/findability/index.md index 5576616a43..edcb13c491 100644 --- a/content/fair/findability/index.md +++ b/content/fair/findability/index.md @@ -122,8 +122,7 @@ Galaxy’s implementation of findability is holistic, integrating infrastructure Galaxy is available under a small range of licenses: * Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* The [codebase](https://github.com/galaxyproject/galaxy) is licensed under the MIT License * Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt * Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. From 79f947d09d89440d62912bc54d90d4c75b5d8204 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:22:25 +0100 Subject: [PATCH 14/19] license --- content/fair/accessibility/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index 4c0148eae4..bc71fc702b 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -115,8 +115,7 @@ Galaxy’s commitment to accessibility ensures that researchers of all backgroun Galaxy is available under a small range of licenses: * Web contents of usegalaxy.eu are published as Creative Commons Zero v1.0 (CC0-v1.) -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed from 2021-04-07 onwards is licensed under the MIT License -* Work on the [codebase](https://github.com/galaxyproject/galaxy) contributed before 2021-04-07 is licensed under the Academic Free License, v3.0 +* The [codebase](https://github.com/galaxyproject/galaxy) is licensed under the MIT License * Further details of underlying licenses: https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt * Every single tool (currently ~3000) has its own license, which is annotated as part of its conda package or container. From 057e6fe8754fe0f728e6ea98d5029722cbe5d883 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:23:31 +0100 Subject: [PATCH 15/19] proper links Co-authored-by: Saskia Hiltemann --- content/fair/accessibility/index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index bc71fc702b..1092504928 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -92,10 +92,10 @@ Galaxy’s use of Pulsar, a lightweight distributed job execution application, e ## Onboarding and Help Channels Galaxy’s accessibility is reinforced by community support and training resources: -- Galaxy Training Network (GTN): provides interactive tutorials and FAIR training materials to help users get started. +- [Galaxy Training Network (GTN)](https://training.galaxyproject.org): provides interactive tutorials and FAIR training materials to help users get started. - Help channels: users can access support via: - - Matrix chat (e.g., #galaxyproject:matrix.org). - - Help boards (e.g., help.galaxyproject.org). + - Matrix chat (e.g., [#galaxyproject:matrix.org](https://matrix.to/#/#galaxyproject:matrix.org)). + - Help boards (e.g., [help.galaxyproject.org](https://help.galaxyproject.org)). - Dedicated documentation and video tutorials. ## Outreach and Inclusivity From 9deb0332265738ef8e7e6217ec1fc1aa3063fb8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:24:14 +0100 Subject: [PATCH 16/19] highlight keyword Co-authored-by: Saskia Hiltemann --- content/fair/accessibility/index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index 1092504928..58b8ba95fd 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -16,9 +16,9 @@ Galaxy’s architecture is based on community-driven initiatives and integration Galaxy is designed to be accessible by default, offering multiple entry points and interfaces to accommodate users with varying levels of technical skill. The platform’s open-source nature ensures transparency, customisability, and community-driven innovation. Its architecture allows for deployment in diverse contexts, from public servers to private, and institution-specific instances. Key features enabling accessibility include: -- Open-source design: Galaxy’s codebase is publicly available (https://github.com/galaxyproject), allowing anyone to deploy, modify, or extend the platform. -- Subdomains and Labs: Galaxy supports community-specific subdomains (e.g., for genomics, earth system science, or ecology) and Galaxy Labs for specialised scientific fields. -- Multi-lingual and multi-interface support: Users can interact with Galaxy via web interfaces, APIs, or interactive environments (e.g., RStudio, Jupyter). +- **Open-source design:** Galaxy’s codebase is publicly available (https://github.com/galaxyproject), allowing anyone to deploy, modify, or extend the platform. +- **Subdomains and Labs:** Galaxy supports community-specific subdomains (e.g., for genomics, earth system science, or ecology) and Galaxy Labs for specialised scientific fields. +- **Multi-lingual and multi-interface support:** Users can interact with Galaxy via web interfaces, APIs, or interactive environments (e.g., RStudio, Jupyter). # Scope and User Base From 8dca99f4f705823abb78316ab1ebdd4863c9bf24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:32:53 +0100 Subject: [PATCH 17/19] add Dropbox and GD --- content/fair/accessibility/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index 58b8ba95fd..57a5a8f0eb 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -55,7 +55,7 @@ Users can export data to: Galaxy’s object stores allow for flexible storage solutions: - Institution-funded storage (e.g., de.NBI-cloud for European users). -- User-owned storage (e.g., AWS, GCS, S3, iRODS), which can be integrated into Galaxy instances. +- User-owned storage (e.g., AWS, GCS, S3, iRODS, Dropbox, and Google Drive), which can be integrated into Galaxy instances. # Tool Accessibility: Usable, Annotated, and Validated ## A Rich Ecosystem of Accessible Tools From 44a7cbb21ad2e24bbd4ef0a1d3d05afe20aa8688 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marie=20Joss=C3=A9?= <84919248+Marie59@users.noreply.github.com> Date: Thu, 12 Mar 2026 14:45:30 +0100 Subject: [PATCH 18/19] add BYOD --- content/fair/accessibility/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index 57a5a8f0eb..0e718d18d4 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -48,7 +48,7 @@ Galaxy’s file-sources and object stores enable access to: **Data Export: Sharing and Archiving** Users can export data to: -- Standard repositories (e.g., ENA for nucleotide sequences). +- Standard repositories with user-defined repositories via BYOD (Bring Your Own Data) across scientific disciplines, such as, ENA (genomics/omics), Zenodo (multi-domain/generalist), and RSpace (electronic lab notebooks and collaborative platforms) - Writable file sources (e.g., FTP, S3, WebDAV). **Object Stores: Scalable and User-Owned Storage** From 7df6050b8ac9711e8c2b92ba8bb14b770208a774 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 12 Mar 2026 21:41:54 +0100 Subject: [PATCH 19/19] remove some redundancies --- content/fair/accessibility/index.md | 10 ++++------ content/fair/findability/index.md | 10 ++++------ content/fair/index.md | 13 +++++++------ content/fair/interoperability/index.md | 7 ++++--- content/fair/reusability/index.md | 10 ++++------ 5 files changed, 23 insertions(+), 27 deletions(-) diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md index 0e718d18d4..50f7f2dc2d 100644 --- a/content/fair/accessibility/index.md +++ b/content/fair/accessibility/index.md @@ -1,13 +1,11 @@ --- title: Galaxy and Accessibility -highlight: true +tease: | + Galaxy combines human-friendly interfaces with machine-readable metadata, standard APIs, portable tool execution, + and community training. That makes FAIR usable both for researchers working interactively and for systems integrating + Galaxy programmatically across larger digital research ecosystems. --- -Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. - -
ELIXIR RIR logo
-
- Galaxy embodies the FAIR “A” principle (Accessibility) by providing an open, inclusive, and technically robust platform that ensures research tools, workflows, and data are available, usable, and adaptable to a diverse global user base. Accessibility in Galaxy is not limited to technical access, it encompasses open-source design, flexible authentication, multi-modal interfaces, distributed computing, and data integration with standard repositories and cloud infrastructures. Galaxy’s architecture is based on community-driven initiatives and integration with global standards and services. This page highlights how this architecture allows to lower barriers to entry for researchers, educators, and data stewards, regardless of their technical expertise or institutional affiliation. diff --git a/content/fair/findability/index.md b/content/fair/findability/index.md index edcb13c491..4af5b264af 100644 --- a/content/fair/findability/index.md +++ b/content/fair/findability/index.md @@ -1,13 +1,11 @@ --- title: Galaxy and Findability -highlight: true +tease: | + Galaxy combines human-friendly interfaces with machine-readable metadata, standard APIs, portable tool execution, + and community training. That makes FAIR usable both for researchers working interactively and for systems integrating + Galaxy programmatically across larger digital research ecosystems. --- -Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. - -
ELIXIR RIR logo
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- Galaxy is an open-source platform for scientific data analysis and sharing. It operationalises the FAIR “F” principle (Findability) through a combination of technical, organisational, and community-driven measures. These ensure that tools, workflows, datasets, and other research objects are easy to find and access by users and machines. This page highlights Galaxy’s findability mechanisms, their alignment with Research Data Management (RDM) principles, and their integration with interoperability frameworks such as those promoted by ELIXIR, GA4GH, and EOSC. diff --git a/content/fair/index.md b/content/fair/index.md index 57e42e7f4e..c7fa6e300b 100644 --- a/content/fair/index.md +++ b/content/fair/index.md @@ -1,11 +1,12 @@ --- title: Galaxy and the FAIR principles -highlight: true +tease: | + Galaxy combines human-friendly interfaces with machine-readable metadata, standard APIs, portable tool execution, + and community training. That makes FAIR usable both for researchers working interactively and for systems integrating + Galaxy programmatically across larger digital research ecosystems. --- -The FAIR (Findable, Accessible, [Interoperable](/fair/interoperability/), Reusable) principles emphasize machine-actionability. -The main objective of FAIR is to increase data reuse by researchers. The core concepts of the FAIR principles are based on good scientific practice and intuitively grounded. - - - +Galaxy turns FAIR from an abstract acronym into daily research infrastructure. Across the project and the public +usegalaxy.* services, researchers can discover well-described tools and workflows, access data through open +interfaces, exchange research objects through shared standards, and rerun analyses with preserved provenance. diff --git a/content/fair/interoperability/index.md b/content/fair/interoperability/index.md index 315b7d7599..fc65b96a0f 100644 --- a/content/fair/interoperability/index.md +++ b/content/fair/interoperability/index.md @@ -1,10 +1,11 @@ --- title: Galaxy and Interoperability -highlight: true +tease: | + Galaxy combines human-friendly interfaces with machine-readable metadata, standard APIs, portable tool execution, + and community training. That makes FAIR usable both for researchers working interactively and for systems integrating + Galaxy programmatically across larger digital research ecosystems. --- -Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. -
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diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md index 5eb73e1b19..61cb6fc6e4 100644 --- a/content/fair/reusability/index.md +++ b/content/fair/reusability/index.md @@ -1,13 +1,11 @@ --- title: Galaxy and Reusability -highlight: true +tease: | + Galaxy combines human-friendly interfaces with machine-readable metadata, standard APIs, portable tool execution, + and community training. That makes FAIR usable both for researchers working interactively and for systems integrating + Galaxy programmatically across larger digital research ecosystems. --- -Galaxy as both a project and a platform facilitates FAIR research, addressing common needs, invoking available standards and contributing to several upstream projects. - -
ELIXIR RIR logo
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- Galaxy operationalises the FAIR “R” principle (Reusability) by providing technical, organisational, and community-driven mechanisms that ensure research objects, such as tools, workflows, histories, and visualisations, can be shared, reproduced, and adapted across diverse scientific contexts. Reusability in Galaxy is about preserving provenance, resolving dependencies, and enabling long-term reproducibility, all while adhering to open standards and best practices in Research Data Management (RDM). Galaxy’s architecture relies on container technologies, provenance tracking, and community-driven quality assurance frameworks. This architecture fosters a culture of reusable, high-quality, and sustainable research.