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Ten common misconceptions about Galaxy (and why they are wrong!)
16 references·0 citing·33 second hop
Ten common misconceptions about Galaxy (and why they are wrong!) (2026)Ten common misconceptions about Galaxy (a…The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)The Galaxy platform for acces…For long-term sustainable software in bioinformatics (2024)For long-term sustainable sof…The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond (2023)The Planemo toolkit for devel…Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (2022)Inverting the model of genomi…Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Reproducible, scalable, and s…Ready-to-use public infrastructure for global SARS-CoV-2 monitoring (2021)Ready-to-use public infrastru…GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians (2021)GalaxyTrakr: a distributed an…On the lifetime of bioinformatics web services (2020)On the lifetime of bioinforma…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The Galaxy platform for acces…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…Assessing the not-invented-here syndrome: Development and validation of implicit and explicit measurements (2017)Assessing the not-invented-he…An architecture for genomics analysis in a clinical setting using Galaxy and Docker (2017)An architecture for genomics …Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics (2014)Workflow4Metabolomics: a coll…BioBlend: automating pipeline analyses within Galaxy and CloudMan (2013)BioBlend: automating pipeline…Galaxy: A platform for interactive large-scale genome analysis (2005)Galaxy: A platform for intera…Harnessing cloud computing with Galaxy Cloud (2011)Next-generation sequencing data interpretation: enhancing reproducibility and accessibility (2012)Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers (2017)DagOn*: Executing Direct Acyclic Graphs as Parallel Jobs on Anything (2018)An efficient pattern-based approach for workflow supporting large-scale science: The DagOnStar experience (2021)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics (2017)PhenoMeNal: processing and analysis of metabolomics data in the cloud (2018)Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing (2019)The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Towards FAIR principles for research software (2019)Towards reproducible computational drug discovery (2020)Snakemake—a scalable bioinformatics workflow engine (2012)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)Singularity: Scientific containers for mobility of compute (2017)Sustainable data analysis with Snakemake (2021)Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists (2010)Accelerating bioinformatics implementation in public health (2023)Nextflow enables reproducible computational workflows (2017)The nf-core framework for community-curated bioinformatics pipelines (2020)Spatial machine learning: new opportunities for regional science (2021)An AI Agent for Fully Automated Multi‐Omic Analyses (2024)Empowering bioinformatics communities with Nextflow and nf-core (2025)Bioconductor: open software development for computational biology and bioinformatics (2004)CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis (2021)From biomedical cloud platforms to microservices: next steps in FAIR data and analysis (2022)Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update (2026)Sustainable data analysis with Snakemake (2021)Applying the FAIR Principles to computational workflows (2025)WorkflowHub: a registry for computational workflows (2025)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022)
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References

  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2005Galaxy: A platform for interactive large-scale genome analysis2,027 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited
  • 2024The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update958 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2014Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics501 cited
  • 2021Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers228 cited
  • 2022Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space143 cited
  • 2013BioBlend: automating pipeline analyses within Galaxy and CloudMan96 cited
  • 2021GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians92 cited
  • 2017Assessing the not-invented-here syndrome: Development and validation of implicit and explicit measurements54 cited
  • 2020On the lifetime of bioinformatics web services50 cited
  • 2021Ready-to-use public infrastructure for global SARS-CoV-2 monitoring24 cited

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2023
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
14 cited
  • 2017An architecture for genomics analysis in a clinical setting using Galaxy and Docker12 cited
  • 2024For long-term sustainable software in bioinformatics11 cited
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