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Galaxy at JOBIM

By Bérénice Batut, Anthony Bretaudeau, Gildas Le Corguillé, Björn Grüning

July 21, 2025

The JOBIM conference, the annual event of the French bioinformatics and biostatistic community, brought together researchers, educators, and innovators in bioinformatics to discuss cutting-edge tools, workflows, and collaborative efforts. Among the highlights of this year's event was the significant presence of Galaxy. This blog post explores the key contributions, presentations, and innovations centered around Galaxy at JOBIM 2025.

Keynote: From Genomes to Galaxies—The Evolution of Scalable Open Data Analysis

The keynote address by Björn, on behalf of the Global Galaxy community, was highly appreciated. Björn provided a compelling overview of how Galaxy has evolved over two decades into a scalable and accessible platform for open data analysis. From genomics to astronomy, Galaxy’s versatility has enabled researchers worldwide to tackle complex computational challenges while fostering collaboration and reproducibility.

The image depicts a presentation slide about a consortium focused on antibiotic resistance in France. It highlights a collaboration of 43 partners, including various National Reference Centers, aimed at detecting and managing antibiotic resistance. The slide features a map of France with marked locations indicating the consortium's reach. It outlines controlled workflows for antibiotic resistance detection, showcasing tools and software used at different stages such as Quality & Contamination Control, Assembly, Annotation, and AMR Gene Detection, with specific tools like Kraken2, Shovill, and ABRicate mentioned. The platform is powered by Galaxy France and is designed to analyze, store, interconnect, and support the surveillance of antibiotic resistance. Additionally, the slide includes a screenshot of the ABRomics web application interface and a world map showing the distribution of antibiotic resistance samples. The presentation appears to be part of a conference or seminar, with a speaker visible on the right side of the image.

Björn emphasized that Galaxy's success lies in its ability to empower both novice users and advanced bioinformaticians. Its user-friendly interface, extensive library of tools, and commitment to open science have made it a go-to platform for diverse scientific communities, including 'omics, ecology and astronomy.

Contributions from the French Galaxy Working Group

The French Galaxy Working Group animated by the IFB/ELIXIR-FR showcased the breadth of their contributions through several posters and presentations:

  • "Exploring the Richness of the French Galaxy Ecosystem" [Poster]

    Bérénice, Gildas, and Anthony presented a detailed analysis of the French Galaxy ecosystem. Their work underscored the diversity of tools, workflows, and community-driven initiatives that have made France a hub for Galaxy innovation.

  • "Breaking Myths: The Reality of Galaxy's Capabilities and Impact" [Poster]

    Gildas, Anthony, Björn, and Bérénice addressed common misconceptions about Galaxy. The poster highlighted how the platform is not just a tool for data analysis but also a powerful enabler of reproducible research, community-driven development, and educational outreach.

  • "Galaxy Training: A powerful framework for teaching!" [Poster]

    Bérénice and Björn demonstrated how Galaxy serves as an invaluable resource for teaching bioinformatics, especially via the Galaxy Training Network. The platform's interactive environment allows educators to create engaging workflows that teach students about data analysis, reproducibility, and best practices in computational biology.

  • "Genome Annotation Tooling in Galaxy" [Poster]

    Romane and Anthony highlighted contributions from the EuroScienceGateway project to improve genome annotation workflows within Galaxy. These advancements enhance the platform's utility for researchers studying genomics and evolutionary biology.

  • "Galaxy as a Service (GaaS)" [Poster]

    Rémi and Juliette introduced GaaS, a TypeScript toolkit designed for developers who want to build custom web applications powered by Galaxy. This innovation bridges the gap between Galaxy's robust analysis capabilities and modern web development practices.

UseGalaxy.fr was also highlighted by Anthony and Bérénice in the IFB presentation during the Network Presentations session.

The image depicts a scene at a conference. In the foreground, two individuals are engaged in conversation, with one person pointing upwards, possibly drawing attention to something of interest. Both individuals are wearing lanyards with badges. Above them, a large poster titled 'Breaking Myths: The Reality of Galaxy's Capabilities and Impact' is prominently displayed. The poster is detailed with various sections, each likely describing different aspects or capabilities of the Galaxy platform, and is adorned with logos of associated organizations such as INRAE, IFB, and others. The background shows a few more attendees walking or standing, contributing to the bustling atmosphere of the event.

The image depicts a woman standing next to a poster presentation at scientific conference. The woman is wearing a light green dress and a lanyard with a name badge. The poster behind her is titled 'A powerful framework for teaching!' and focuses on the Galaxy Training Network (GTN). The poster provides detailed information about the GTN, including its purpose, achievements, and resources. Key points highlighted on the poster include the collection of FAIR (Findable, Accessible, Interoperable, and Reusable) training materials, with statistics such as over 35 topics, 450+ tutorials, contributions from 490+ contributors, and 3,970+ feedback entries. Additionally, the poster mentions the organization of massive, online, and worldwide training events, with over 220 videos, 140+ hours of recordings, and participation from 130+ instructors and 10,000+ registrants. The poster also acknowledges various supporting institutions and projects, such as the Institut Français de Bioinformatique (IFB), Erasmus+, and INRAE. The background shows a busy conference setting with other attendees walking and engaging in discussions.

The image depicts a scene from a conference presentation. Two presenters are standing at the front of a lecture hall, actively engaged in delivering their talk. The presenter on the left is standing behind a podium with a laptop, while the presenter on the right is gesturing towards a projected slide on a large screen behind them. The slide is titled 'Madbot and its plugins' and features a diagram illustrating the interaction between different components such as a data plugin, DublinCore, Zenodo, and ENA (European Nucleotide Archive). The audience, seated and facing the presenters, appears attentive and engaged, with some individuals using laptops. The setting suggests a professional and academic environment focused on scientific or technical discussions.

The image depicts a scene at a scientific conference. In the foreground, a man wearing a green t-shirt and a conference lanyard stands next to a poster presentation. The poster, titled 'ABRomics-analysis: Developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform,' details a study on antibiotic resistance. It compares genomics and metagenomics, outlining their objectives, sequencing methods, advantages, limitations, and applications. The poster also describes three complementary metagenomic workflows: raw reads, gene collection, and MAG (Metagenome-Assembled Genome) reconstruction, all integrated with the Galaxy platform. The background shows a busy conference environment with other attendees and posters, indicating a professional and academic setting focused on scientific research and collaboration.

The image depicts a scene at a scientific conference. In the foreground, a group of attendees is gathered around a poster presentation. The poster, titled 'Building a Standardized Database for Honey Bee Microbiome: Addressing Metadata and Data Comparability Gaps,' is displayed on a metal grid. The poster includes sections such as Background, Problem, Solution, Preliminary Results & Challenges, and Future Directions, detailing the research on honey bee microbiomes. The presenters and attendees appear engaged in discussion, with one woman in a red dress pointing to specific parts of the poster, possibly explaining the research findings or methodology. The background shows a busy conference environment with other attendees walking and engaging in discussions, indicating a professional and academic setting focused on scientific research and collaboration.

ABRomics: Antibiotic Resistance Surveillance and Resarch with Galaxy

ABRomics, a project centered on antibiotic resistance (AMR) surveillance, was another highlight of the conference:

Mention of Galaxy in Other Projects

Galaxy's versatility was evident in its mention across various projects:

  • "Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis" [Talk]

    This talk by David Couvin emphasized the use of Galaxy for training purposes, particularly in an island context, focusing on microbial omics data analysis

  • "Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks" [Talk]

    The Met4J tools were showcased as a workflow suite and available as tools in Galaxy, facilitating graph-based analysis of metabolic networks.

  • "Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context" [Talk]

    Madbot was presented as an online tool that connects with Galaxy, alongside platforms like ENA and OMERO, to manage and share scientific data, promoting open science standards.

  • "Ten years of the Pasteur's Bioinformatics and Biostatistics Hub: achievements and perspectives" [Talk]

    The Pasteur hub highlighted its work including its Galaxy instance, designed to support community bioinformatics analyses and contributions to ELIXIR's tool platform.

  • "vvv2_display: Galaxy Workflows for Variant Calling and Annotation" [Poster]

    Alexandre Flageul and colleagues highlighted how Galaxy workflows are being used to compute, summarize, and visualize variant calling and annotations in viral genomes. Tools like vvv2_align_SE and vvv2_display are available on the Galaxy Toolshed, making them accessible to a wide audience.

  • "SIDURI: A User-Friendly Portal for Fermentation Data Analysis" [Poster]

    The SIDURI project integrates Galaxy into its workflow management system, enabling users to analyze fermentation data through an intuitive interface. This integration demonstrates Galaxy's adaptability as a platform for diverse scientific domains.

  • "IFB/ELIXIR-FR contributions to the ELIXIR Training Platform" [Poster]

    French contributions to the ELIXIR Training Platform were also highlighted, with a focus on the Galaxy Training Network (GTN). These efforts underscore the importance of training and education in fostering a skilled bioinformatics workforce.

  • "Building a Standardized Database for Honey Bee Microbiome: Addressing Metadata and Data Comparability gaps"

    Bérénice and Nadia presented collaborative work between AuBi platform and the Host-Parasite team at LMGE, focusing on data comparability and metadata quality in microbiome research. Preliminary efforts included aggregating metadata and developing standardized Galaxy pipelines. Key challenges identified were the lack of detailed metadata and standardized workflows for dataset reanalysis. The project aims to build a robust bee microbiome database using advanced data analysis.

Conclusion

JOBIM 2025 was a testament to the enduring impact and versatility of Galaxy as a platform for open data analysis. From keynote addresses to posters, demo, and talk, the conference showcased how Galaxy continues to empower researchers, educators, and innovators across diverse fields. As the global community of Galaxy users grows, its role in advancing reproducible science, supporting education, and addressing real-world challenges like antibiotic resistance will only continue to expand.

Galaxy's journey from genomics to galaxies is far from over—it remains a beacon of innovation and collaboration in bioinformatics.

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