Publication Details

Category Text Publication
Reference Category Conference papers
DOI 10.7490/f1000research.1119764.1
Licence creative commons licence
Title (Primary) Galaxy CoDex for finding tools, workflows, and training [version 1]
Title (Secondary) Galaxy Community Conference 2024
Author Batut, B.; Bacon, W.; Zierep, P.; Bernt, M. ORCID logo ; Soranzo, N.; Gustafsson, J.
Source Titel F1000Research
Year 2024
Department COMPBC
Volume 13
Page From 705 (slides)
Language englisch
Topic T9 Healthy Planet
Keywords Galaxy; Community; Annotation; Tool; Training; Workflow
Abstract Galaxy offers an ecosystem containing thousands of tools, hundreds of tutorials, and a currently unknown number of workflows. The abundance of locations where these resources can be found, coupled with their diverse and fragmented nature, makes it incredibly difficult for Galaxy users to find and reuse tools, or to filter for all resources available for a specific research community, domain, or research area. By extension, it is also difficult for Special Interest Groups (SIG) to give visibility to their collective works.

To improve the findability of tools, a pipeline (Galaxy Tool Metadata Extractor) was developed at the BioHackathon Europe 2023 to collect Galaxy suites from different locations, automatically extract their metadata (including bio.tools identifier and EDAM ontology concepts), and display this information as an interactive list that can be filtered to display tools that are relevant to a specific research community or domain (DOI: 10.37044/osf.io/qjbxc). 

In developing this pipeline, two challenges were apparent: 1) many tools are missing proper bio.tools or EDAM annotations, and 2) a Galaxy SIG offers more resources than just tools. In fact, SIGs also offer training materials and workflows, which are often dispersed and poorly annotated. 

During the BioHackathon Europe 2023, and in a second community-hosted online hackathon in 2024, the microGalaxy SIG tackled the first challenge by working on tool annotation, thereby improving the EDAM annotations for more than 200 tools, and annotating more than 30 tutorials with EDAM concepts. Additional communities, including single-cell and imaging SIGs, have also started similar annotation efforts.

To address the second challenge, and aggregate the sum of resources available to a SIG, the Galaxy Tool Metadata Extractor is now being extended to create the Galaxy Communities Dock or Galaxy CoDex. Galaxy CoDex includes a centralised webpage template and files that will enable domain communities to rapidly aggregate, curate, integrate, display, and launch relevant tools, workflows, and training on different Galaxy servers. 

This catalog and its implementation form the foundation of a wider initiative - spearheaded by the Galaxy Community Board and two communities in particular - to unify resources across Galaxy servers.

In this talk, we present the work done over the last year to build this catalog. Importantly, we also want to make the wider community aware of this ongoing effort and invite additional contributors: (i) new communities or SIGs that can be included in the catalog and give feedback on its structure and function, and (ii) Galaxy developers to help us establish and implement best practice recommendations for resource annotation at different levels in the Galaxy ecosystem (e.g. adding an EDAM Topics field to the workflow best practices dialogue in the Galaxy interface).
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=29396
Batut, B., Bacon, W., Zierep, P., Bernt, M., Soranzo, N., Gustafsson, J. (2024):
Galaxy CoDex for finding tools, workflows, and training [version 1]
Galaxy Community Conference 2024
F1000Research 13
F1000 Research Ltd, London, 705 (slides) 10.7490/f1000research.1119764.1