Misconceptions about Galaxy debunked by the (French) Galaxy Community - Archive ouverte HAL
Communication Dans Un Congrès Année : 2024

Misconceptions about Galaxy debunked by the (French) Galaxy Community

Résumé

Background Open science computing constitutes a vast, interconnected domain, characterized by its complexity and constant evolution. With computational tools and methods continually advancing, individuals often find it challenging to grasp the entirety of this field. Workflow managers such as Galaxy, Nextflow, Snakemake, and numerous others offer a solution by enabling scientists to swiftly construct intricate and reproducible pipelines, alleviating the necessity to comprehend their inner workings entirely. This approach enables researchers to concentrate on high-value data analysis, freeing them from the complexities of building workflows from scratch. Established in 2005, Galaxy offers a workflow manager that is continually maintained and expanded to support analysis across diverse domains. Bolstered by vibrant global communities, Galaxy undergoes continuous refinement, ensuring its adaptability and relevance in various scientific contexts. As a free, open-source platform, Galaxy facilitates data analysis, workflow authoring, training and education, tool publication, infrastructure management, and more. Galaxy is well adopted in the French ecosystem with 10+ servers and UseGalaxy.fr, the French UseGalaxy server. Despite this wide adoption and support by ample training resources, Galaxy faces persistent misconceptions. These include the belief that it's exclusively for genomics and challenging to use. To address these misconceptions, the Galaxy Community conducted a user survey. Results Through this survey, the Galaxy Community commenced the process of dispelling common misconceptions. The French Galaxy Community, inspired by these debunked myths, further advances this endeavor by gathering and showcasing Galaxy initiatives within the French ecosystem. “Galaxy is only useful for genome scientists” - UseGalaxy.fr offers 3k+ tools and hosts several community-specific subdomains beyond genomics (e.g. ecology, workflow4metabolomics). “Galaxy does not scale to large and complex problems” - UseGalaxy.fr is involved in European efforts such as EuroScienceGateway but also many national projects. It is for example the central piece for ABRomics, the national platform for antimicrobial resistance surveillance: all data on this platform is processed using standardized Galaxy workflows run on UseGalaxy.fr. “Galaxy offers nothing to technically capable informaticians who can write their own analysis code” - Hosted by IFB Core Cluster, UseGalaxy.fr offers 8300 CPU cores, 52 TB of RAM, and GPU cards. Several Interactive tools (GxIT) like Jupyter Notebook, AlphaFold, and Helixer, are available. More importantly, Galaxy offers a platform for versioned, reproducible data analysis, which can be easily shared with others, a powerful workflow manager with metadata annotation to encourage FAIR workflows, an access to 100+ standardized workflows available from two workflow registries (WorkflowHub[4] and Dockstore[5]), and a powerful API with openAPI and a Python package (BioBlend). “Galaxy is hard to learn and hard to use.” - Galaxy is a powerful and complex system that can be overwhelming when coming to an unfamiliar web interface, with unfamiliar terminology for the first time. But its interface has been improved, e.g. the workflow editor with workflow annotation. Galaxy offers also 400+ tutorials available via the Galaxy Training Network[6,7]. UseGalaxy.fr also offers the Training Infrastructure as a Service (TIaaS)[8]. Since February 2022, this service has offered 550+ computing days to 70+ events reaching 1700+ learners. “Galaxy is only useful for teaching, not real scientific analyses” - Galaxy is widely used given the 30+ publications per week using Galaxy. As mentioned, it is the central piece of projects like ABRomics or the Vertebrate Genomes Project (VGP)[9]. “Galaxy is neither popular with, nor widely used by real scientists” - Since 2021, 6k+ users ran 3.6M+ jobs on UseGalaxy.fr. “Galaxy is free, so there cannot be professional staff offering quick and helpful support.” - All support on UseGalaxy.fr is done as a community effort, using the public Discourse hosted by IFB (https://community.france-bioinformatique.fr/), with the support of a team of 6 IFB members from multiple regional platforms “​​Galaxy is free, so there cannot be useful documentation since nobody is paid to write, maintain, or deliver it.” - Galaxy offers documentation for all its pieces and provides plenty of tutorials. “Galaxy is free, so it cannot be good because professional engineers are not being paid to fix bugs and develop enhancements.” - UseGalaxy.fr is co-administered by a team of 6 IFB members from multiple regional platforms. “Galaxy cannot be sustainable in the long run, because no commercial organisation is managing it” - UseGalaxy.fr is more sustainable than being managed by a commercial organisation: it is supported by IFB and several administrative supervisions with permanent positions “Galaxy tools or omics support in Galaxy are dated and not up-to-date” - Tools on UseGalaxy.fr are installed using a standard GitLab repository and auto-updated by a bot (IFBOT) once a week. Conclusions Galaxy faces persistent misconceptions, such as Galaxy's purported limitations in scaling to complex problems, its perceived lack of value for technically skilled informaticians, and its difficulty of use. The Galaxy community addresses these misconceptions, but also misconceptions about its utility only for teaching, its lack of popularity among scientists, and doubts about its sustainability without commercial backing. The survey's findings and debunking work shed light on Galaxy's diverse applications and advantages, emphasizing its central role in open science computing.
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hal-04694551 , version 1 (11-09-2024)

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  • HAL Id : hal-04694551 , version 1

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Romane Libouban, Eva Mercier, Thomas Chaussepied, Bérénice Batut, Anthony Bretaudeau, et al.. Misconceptions about Galaxy debunked by the (French) Galaxy Community. JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024, TOULOUSE, France. pp.1-28. ⟨hal-04694551⟩
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