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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
3 references·11 citing·25 second hop
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update (2020)The Galaxy platform for accessible, repro…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…Singularity: Scientific containers for mobility of compute (2017)Singularity: Scientific conta…Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)Jupyter Notebooks – a publish…Empowering bioinformatics communities with Nextflow and nf-core (2025)Empowering bioinformatics com…HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data (2024)HiOmics: A cloud-based one-st…Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice (2023)Building Domain-Specific Mach…Ten simple rules and a template for creating workflows-as-applications (2022)Ten simple rules and a templa…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…The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols (2021)The Dockstore: enhancing a co…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…Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine (2021)Galaxy-ML: An accessible, rep…Bioinformatics tools developed to support BioCompute Objects (2021)Bioinformatics tools develope…Bioimage analysis workflows: community resources to navigate through a complex ecosystem (2021)Bioimage analysis workflows: …Snakemake—a scalable bioinformatics workflow engine (2012)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)Design Patterns: Elements of Reusable Object-Oriented Software (1994)The nf-core framework for community-curated bioinformatics pipelines (2020)Packaging and containerization of computational methods (2024)A terminology for scientific workflow systems (2025)Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update (2026)Dissemination of scientific software with Galaxy ToolShed (2014)Artificial intelligence faces reproducibility crisis (2018)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022)Nextflow enables reproducible computational workflows (2017)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Spatial machine learning: new opportunities for regional science (2021)An AI Agent for Fully Automated Multi‐Omic Analyses (2024)Bioconductor: open software development for computational biology and bioinformatics (2004)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)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)SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research (2017)Open science challenges, benefits and tips in early career and beyond (2019)NeuroKit2: A Python toolbox for neurophysiological signal processing (2021)Sustainable data analysis with Snakemake (2021)The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond (2023)
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References

  • 2016Jupyter Notebooks – a publishing format for reproducible computational workflows3,069 cited
  • 2017Singularity: Scientific containers for mobility of compute2,734 cited
  • 2018Bioconda: sustainable and comprehensive software distribution for the life sciences1,652 cited

Cited by

  • 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
  • 2025Empowering bioinformatics communities with Nextflow and nf-core64 cited
  • 2021The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols34 cited
  • 2021Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine28 cited
  • 2021Ready-to-use public infrastructure for global SARS-CoV-2 monitoring24 cited
  • 2022Ten simple rules and a template for creating workflows-as-applications24 cited
  • 2021Bioimage analysis workflows: community resources to navigate through a complex ecosystem22 cited
  • 2024HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data15 cited
  • 2021Bioinformatics tools developed to support BioCompute Objects12 cited
  • 2023

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Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice
10 cited