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Project 11: Galaxy CoDex - Ensuring Galaxy community sustainability through resource aggregation and annotation

Abstract

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."

Scope/Tasks

  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 (microGalaxy, single-cells and yours?)
  3. Establishing ongoing resource annotation best practices within the Galaxy ecosystem

Useful skills

GitHub, Markdown

  1. Improve the infrastructure of the Galaxy Codex: Python, Web development, Jekyll, Galaxy tools, Galaxy workflows, Databases
  2. Annotation of community resources: Interest in microbiology, single-cells, or proteomics
  3. Annotation best practices: EDAM, Galaxy tools, workflows

Coordination

We use an organization document to share all useful links (especially to coordination spreadsheets), share detailed tasks, keep notes, and coordinate.

Schedule

The schedule is quite flexible. There is no requirement to join the whole week. 1 daily stand-up (will be run to coordinate with online participants and the Australian outpost

Monday, November 4th

Time (CET) Topic
15:30-16:00 Presentation of the process to link Galaxy tools to bio.tools and improve bio.tools annotations
16:00-18:00 Hacking

Tuesday, November 5th - Thursday, November 7th

Time (CET) Topic
8:30-10:00 Stand-up & New participant onboarding
10:00-12:30 Hacking with open Zoom
13:45-15:30 Hacking

Friday, November 8th

Time (CET) Topic
8:30-10:00 Stand-up & Outcome collection

Leads

Bérénice Batut, Wendi Bacon