diff --git a/content/fair/accessibility/index.md b/content/fair/accessibility/index.md new file mode 100644 index 0000000000..50f7f2dc2d --- /dev/null +++ b/content/fair/accessibility/index.md @@ -0,0 +1,139 @@ +--- +title: Galaxy and Accessibility +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 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 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. + +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://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). + +**Data Export: Sharing and Archiving** + +Users can export data to: +- 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** + +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, Dropbox, and Google Drive), 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, 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 +## 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 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. + +# Community Support and Training +## Onboarding and Help Channels + +Galaxy’s accessibility is reinforced by community support and training resources: +- [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](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 + +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 authorisation and 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.) +* 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. + +## 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. diff --git a/content/fair/findability/index.md b/content/fair/findability/index.md new file mode 100644 index 0000000000..4af5b264af --- /dev/null +++ b/content/fair/findability/index.md @@ -0,0 +1,146 @@ +--- +title: Galaxy and Findability +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 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.) +* 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. + +## 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. 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 b93540f5c7..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. -
ELIXIR RIR logo

@@ -115,8 +116,7 @@ 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. diff --git a/content/fair/reusability/index.md b/content/fair/reusability/index.md new file mode 100644 index 0000000000..61cb6fc6e4 --- /dev/null +++ b/content/fair/reusability/index.md @@ -0,0 +1,116 @@ +--- +title: Galaxy and Reusability +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 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 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. + +# 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.) +* 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. + +## 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.