Finding workflows in the Galaxy universe: integrating a global ecosystem using workflow registries
Authors/Creators
- 1. Australian BioCommons, University of Melbourne, Australia
- 2. Earlham Institute, UK
- 3. University of Freiburg, Germany
- 4. Pennsylvania State University, USA
- 5. University of Manchester, Manchester, UK
- 6. Australian BioCommons, QCIF, Australia
- 7. QCIF, University of Queensland, Australia
- 8. Australian BioCommons, QCIF, University of Queensland, Australia
- 9. Australian BioCommons, QCIF, University of Queensland, University of Melbourne, Australia
Description
The Galaxy framework democratises the ability to create and maintain complex computational workflows, empowering subject matter experts across diverse research fields to design and run their own analyses without worrying about the underlying infrastructure that makes tool execution in the cloud possible. The underlying framework however does not remove the need to invest expertise, time and effort in the development, testing and optimisation of these workflows. It is this investment that underpins needing to make workflows findable, accessible, interoperable and reusable (FAIR): creators of workflows should be able to effectively share their work and see it reused and cited, while workflow users should be facilitated to find these workflows effortlessly.
Galaxy already excels in the reusability of workflows that are described in a standardised way. It is findability that can be challenging, as Galaxy workflows are created within an instance and this does not currently translate to visibility across the more than 130 public servers in the global Galaxy network. In effect, a Galaxy Europe user might replicate a workflow that a user in Australia has already created and vice versa. Wouldn’t the intergalactic neighbourhood seem a bit smaller if the workflow contributions across this neighbourhood were findable? We suggest that workflow visibility across Galaxies is indispensable in the Galaxy universe. Community efforts are leading the way in addressing this for canonical best practice workflows: i.e. through the Intergalactic Workflows Commission (IWC). With the right support, there is also an opportunity to engage the broader research community in this effort and provide clear pathways to make thousands of existing and new Galaxy workflows searchable, understandable and citable.
This poster highlights the key steps a workflow creator in Galaxy can take to make their work findable, well annotated and citable: in doing so it draws together and articulates the breadth of efforts across the Galaxy project related to workflows, including Galaxy workflow best practices and RO-crate export, registration of workflows (IWC and others) on platforms like WorkflowHub and Dockstore, and sustainable maintenance through the use of community templates (IWC, template generators) and the application of tools like LifeMonitor. Our aim is to provide a roadmap for success, whereby currently available platforms, services and tools that improve the visibility and reusability of Galaxy workflows can be clearly described and easily accessible to end users and workflow developers, and also be placed in the context of day-to-day research practice.
We would like this poster to help stimulate discussion at the conference, and continue evolving this guidance material together with the Galaxy and workflow communities. This will allow us to incorporate new and aspirational elements of the ecosystem, ensure that the Galaxy platform can continue supporting established research communities, and provide a compelling case for new users to adopt the Galaxy framework to support their research.
Files
1.12_Finding workflows in the Galaxy universe - slide 1.png
Additional details
References
- The Galaxy Community, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351, https://doi.org/10.1093/nar/gkac247
- Barker, M. et al. (2022). Introducing the FAIR Principles for research software. Sci Data 9, 622. https://doi.org/10.1038/s41597-022-01710-x
- https://usegalaxy.eu/
- IWC - Intergalactic Workflow Commission (2023). https://github.com/galaxyproject/iwc
- https://planemo.readthedocs.io/en/stable/best_practices_workflows.html
- Soiland-Reyes, S. et al. (2022): Packaging research artefacts with RO-Crate. Data Science 5(2) https://doi.org/10.3233/DS-210053
- Goble, C. et al. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. Zenodo https://zenodo.org/record/4605654
- Yuen, D. et al. (2022). dockstore/dockstore: 1.13.1 (1.13.1). Zenodo. https://doi.org/10.5281/zenodo.7259426
- LifeMonitor development team (2023). LifeMonitor (Version 0.11.2) [Computer software]. https://github.com/crs4/life_monitor
- Black M et al. (2021). EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]. F1000Research 2022, 11(ISCB Comm J):1 (poster) (https://doi.org/10.7490/f1000research.1118900.1)
- De Geest, P. (2023). Exporting Workflow Run RO-Crates from Galaxy (Galaxy Training Materials). https://gxy.io/GTN:T00340 Online; accessed Fri Jun 30 2023
- Druskat, S. et al. (2021). Citation File Format (Version 1.2.0) [Computer software]. https://doi.org/10.5281/zenodo.5171937
- Ison, J. et al. (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. doi: 10.1093/nar/gkv1116
- GA4GH (2023). Schemas for the GA4GH Tool Registry API. https://github.com/ga4gh/tool-registry-service-schemas
- ELIXIR (2021). Research Data Management Kit. A deliverable from the EU-funded ELIXIR-CONVERGE project (grant agreement 871075). URL: https://rdmkit.elixir-europe.org
- Workflow Run RO-Crate working group (2023). Workflow Run RO-Crate. https://w3id.org/ro/wfrun