---
title: 'Galaxy CoDex - Ensuring Galaxy community sustainability through resource aggregation and annotation'
title_short: 'BH24EU project 11: Galaxy CoDex'
tags:
- Findability
- Galaxy
- Community-specific Galaxy tools
- Tools
- EDAM
- bio.tools
- Metadata
authors:
- name: Bérénice Batut
orcid: 0000-0001-9852-1987
affiliation: 1, 2, a
- name: Wendi Bacon
orcid:
affiliation: 3, a
- name: Paul Zierep
orcid: 0000-0003-2982-388X
affiliation: 1, a
- name: Matúš Kalaš
orcid: 0000-0002-1509-4981
affiliation: 4
- name: Wai Cheng Thang
orchid: 0000-0002-1480-3563
affiliation: 5, 6
- name: Ove Johan Ragnar Gustafsson
orcid: 0000-0002-2977-5032
affiliation: 7
affiliations:
- name: Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
index: 1
- name: Institut Français de Bioinformatique, CNRS UAR 3601, Évry, France & Mésocentre Clermont-Auvergne, Université Clermont Auvergne, Aubiere, France
index: 2
- name:
index: 3
- name: Department of Informatics, University of Bergen, Norway; and ELIXIR Norway
index: 4
- name: Queensland Cyber Infrastructure Foundation (QCIF), Australia
index: 5
- name: Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia
index: 6
- name: Australian BioCommons, University of Melbourne, Melbourne, Victoria, Australia
index: 7
- name: These authors contributed equally to this work
index: a
date: 8 November 2024
bibliography: paper.bib
event: BH24EU
biohackathon_name: "BioHackathon Europe 2024"
biohackathon_url: "https://biohackathon-europe.org/"
biohackathon_location: "Barcelona, Spain, 2024"
group: Project 11 - Galaxy CoDex - Ensuring Galaxy community sustainability through resource aggregation and annotation
git_url:
authors_short: Bérénice Batut, Wendi Bacon, \emph{et al.}
---

# Introduction

Galaxy hosts a vast array of tools, tutorials, and workflows, with the exact number of workflows remaining uncertain. To address the challenge of enhancing tool visibility within this expansive ecosystem, a pipeline called the Galaxy Tool Metadata Extractor was created during the BioHackathon Europe 2023. This pipeline aggregates Galaxy tool suites from various sources, automatically extracts metadata such as bio.tools identifiers and EDAM ontology, and presents the information in an interactive table. Users can filter this table to find tools relevant to their research community. Throughout development, it was noted that many tools lack EDAM annotations. Efforts by the microbial community during both BioHackathon 2023, and a subsequent community-hosted online hackathon in 2024, have improved EDAM annotations for over 200 tools. However, Galaxy communities also offer training materials and workflows, which, like software, may be scattered across different platforms and lack EDAM annotations.

Building upon the achievements of BioHackathon Europe 2023, this new initiative seeks to expand the capabilities of the existing Galaxy tool list table by introducing the Galaxy Communities Dock (**Galaxy CoDex**). Galaxy CoDex will involve enhancing and implementing webpage templates and files that enable domain communities to efficiently gather, organize, integrate, and deploy pertinent tools, workflows, and training materials across various Galaxy servers. Concurrently, best practices for resource annotation will be developed and integrated into different levels of the Galaxy ecosystem.

In essence, the growth of Galaxy Communities necessitates the adoption of sustainable practices to ensure their continued advancement.

This project aims to achieve three main objectives:

1. **Establishing the infrastructure for Galaxy CoDex** to enhance the discoverability of tools, workflows, and training materials within the Galaxy ecosystem,
2. **Ensuring the sustainability of Galaxy CoDex** by implementing comprehensive resource annotations for communities (e.g. microGalaxy, single-cells), and
3. **Establishing ongoing resource annotation best practices within the Galaxy ecosystem.**

# Methods

## CoDex

The CoDex codebase was improved by multiple enhancements. In preparation of the BioHackathon Europe 2024 two additional community resource collection features were implemented, that collect workflows from workflowhub and Galaxy servers (PR: TODO) as well as training from the Galaxy Training Network (GTN) (PR: TODO).

During the BioHackathon Europe 2024 the codebase was adapted to agree with coding best practices in order to make the future development more sustainable and error prove. Therefore the tool collection function was restuctured to follow object oriented progamming paradigm (PR: TODO), wich was already implemeted for the workflows and training collection functions. Furhermore an initial unittest framework was developed which allows to test individual functions of the CoDex, including using mock API calls to the involved services. This framework ensures, that newl

## Community curation

## Website

* Elixir TK Search Feature

# Outcomes and results

# Conclusion and outlook

# Acknowledgements

This work was developed as part of BioHackathon Europe 2024.
This work was supported by [ELIXIR](https://elixir-europe.org), the research infrastructure for life science data.
This work was supported by the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia funding.

# References