Scripts and data associated with the Microbiology Galaxy Lab (MGL) and microGalaxy 2026 paper

This repository includes all data and scripts needed to produce figures and statisctical information presented in the paper.

Running the MGL locally

docker run --rm -i -t --privileged -p 8080:80 -v ~/export.microbiology/:/export quay.io/galaxy/docker-galaxy-microbiology-lab

Visit the MGL Docker development repository for more details.

Requirements

• Install conda

  $ make install-conda
  

• Create the conda environment

  $ make create-env
  

Usage

Retrieve citations

• Launch Jupyter to access the notebooks to generate graphs

  $ make run-jupyter
  

• Go to http://localhost:8888 (a page should open automatically in your browser)

Update data

• Launch the dedicated script

  $ bash bin/get_data.sh
  

Rebuild figures

bash bin/build_figures.sh

MGL paper's supplementary information (figures, tables, and methods)

This section provides easy access to the MGL paper's figures, extended data, and supplementary materials.

Figures (in docs/figures folder)

• Graphical abstract
• Figure 1: Microbiology Galaxy Lab (MGL) interface (A) in comparison with default Galaxy interfaces on the UseGalaxy server (B, C).
• Figure 2: Citation trends in Galaxy publications and survey results from the microbiology research community (March–September 2023).
• Figure 3: Growth and usability of microbiology-related tool suites, training materials/tutorials, and workflows within the Galaxy ecosystem that are included in the Microbiology Galaxy Lab (MGL).
• Figure 4: Overview of microbiological data analysis tasks with corresponding tool suites and potential analyses available on the MGL.
• Figure 5: Applications of MGL tools and workflows in health, disease, and ecosystem research.

Supplementary information (in docs/supplementary folder)

• Supplementary Figure 1: Microbial Research Topics in Galaxy Publications.
• Supplementary Figure 2: Availability of microbiology-related tool suites within the Galaxy ecosystem.
• Supplementary Figure 3: Usage of microbiology-related tool suites across workflows.
• Supplementary Figure 4: Usage of microbiology-related tool suites across training materials.
• Supplementary Figure 5: Flowchart illustrating the process to select and annotate the microbiology-related publications citing the Galaxy Project's major publication.
• Supplementary Table 1: Features and capabilities of 45 existing user-friendly microbiological data analysis platforms (non-exhaustive list).
• Supplementary Table 2: Anonymous results from the microbiology research community survey conducted between March and September 2023.
• Supplementary Table 3: Publications citing the Galaxy Project from Google Scholar.
• Supplementary Table 4: Publications citing the Galaxy Project from Google Scholar classified as microbiology-related citations.
• Supplementary Table 5: Overview of the 319 microbiology-related tool suites available in the Microbiology Galaxy Lab (MGL).
• Supplementary Table 6: Tool suites corresponding to numbers on Figure 4.
• Supplementary Table 7: Comprehensive list of the 117 microbiology-related workflows available in the Microbiology Galaxy Lab (MGL).
• Supplementary Table 8: Summary of use case submissions collected from survey participants and other highlighted use cases.
• Supplementary Table 9: Comprehensive list of tutorials from the Galaxy Training Network (GTN) dedicated to microbiological data analysis.
• Supplementary Table 10: Overview of microbiology-related training events conducted between 2019 and 2025.
• Supplementary Table 11: Manual binary document-level validation of microbiology-related citation classification.
• Supplementary Table 12: Manual multi-label keyword-level validation of automated microbiology citation classification.
• Supplementary Method 1: List of survey questions shared with the microbiology research community via a Google Form between March and September 2023.
• Supplementary Method 2: microGalaxy Community Roadmap (2026–2030), outlining the strategic priorities, goals, and planned developments for the Microbiology Galaxy Lab (MGL).
• Supplementary Method 3: Template to collect use cases from survey participants who expressed interest in contributing to the planned manuscript.
• Supplementary Method 4: Manual validation framework for automated citation classification.