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The five pillars of computational reproducibility: bioinformatics and beyond
16 references·5 citing·27 second hop
The five pillars of computational reproducibility: bioinformatics and beyond (2023)The five pillars of computational reprodu…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022)The Galaxy platform for acces…Sustainable data analysis with Snakemake (2021)Sustainable data analysis wit…Sustainable data analysis with Snakemake (2021)Sustainable data analysis wit…Replicability, Robustness, and Reproducibility in Psychological Science (2021)Replicability, Robustness, an…Singularity: Scientific containers for mobility of compute (2017)Singularity: Scientific conta…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…A manifesto for reproducible science (2017)A manifesto for reproducible …What does research reproducibility mean? (2016)What does research reproducib…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…Positioning and Power in Academic Publishing: Players, Agents and Agendas (2016)Positioning and Power in Acad…Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)Jupyter Notebooks – a publish…How open science helps researchers succeed (2016)How open science helps resear…Ten Simple Rules for Reproducible Computational Research (2013)Ten Simple Rules for Reproduc…Snakemake—a scalable bioinformatics workflow engine (2012)Snakemake—a scalable bioinfor…Reproducible Research in Computational Science (2011)Reproducible Research in Comp…Study Area Map Generator: A Web-Based Shiny Application for Generating Country-Level Study Area Maps for Scientific Publications (2025)Study Area Map Generator: A W…Molecular biology in the exabyte era: Taming the data deluge for biological revelation and clinical transformation (2025)Molecular biology in the exab…ENCORE: a practical implementation to improve reproducibility and transparency of computational research (2024)ENCORE: a practical implement…Detailed Implementation of a Reproducible Machine Learning-Enabled Workflow (2024)Detailed Implementation of a …Characterising reproducibility debt in scientific software: A systematic literature review (2024)Characterising reproducibilit…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Galaxy: A platform for interactive large-scale genome analysis (2005)Policy: NIH plans to enhance reproducibility (2014)A solution to minimum sample size for regressions (2020)CONSORT 2025 statement: updated guideline for reporting randomised trials (2025)CONSORT 2025 statement: updated guideline for reporting randomised trials (2025)The PRISMA Statement for Reporting Systematic Reviews and Meta-Analyses of Studies That Evaluate Health Care Interventions: Explanation and Elaboration (2009)CONSORT 2010 Statement: updated guidelines for reporting parallel group randomised trials (2010)Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015: elaboration and explanation (2015)The preregistration revolution (2018)Reproducibility: A tragedy of errors (2016)The nf-core framework for community-curated bioinformatics pipelines (2020)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)1,500 scientists lift the lid on reproducibility (2016)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)Applying the FAIR Principles to computational workflows (2025)Increasing value and reducing waste in research design, conduct, and analysis (2014)Reproducibility in Science (2014)An introduction to Docker for reproducible research (2015)Open science challenges, benefits and tips in early career and beyond (2019)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update (2020)NeuroKit2: A Python toolbox for neurophysiological signal processing (2021)Enabling dynamic and intelligent workflows for HPC, data analytics, and AI convergence (2022)Empowering bioinformatics communities with Nextflow and nf-core (2025)
this work references cited by second hop

References

  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2017A manifesto for reproducible science3,368 cited
  • 2016Jupyter Notebooks – a publishing format for reproducible computational workflows3,069 cited
  • 2012Snakemake—a scalable bioinformatics workflow engine2,775 cited
  • 2017Singularity: Scientific containers for mobility of compute2,734 cited
  • 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update2,149 cited
  • 2021Sustainable data analysis with Snakemake1,646 cited
  • 2011Reproducible Research in Computational Science1,446 cited
  • 2016What does research reproducibility mean?1,291 cited
  • 2022The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update1,280 cited
  • 2016Positioning and Power in Academic Publishing: Players, Agents and Agendas935 cited
  • 2013Ten Simple Rules for Reproducible Computational Research875 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2016How open science helps researchers succeed790 cited
  • 2021Sustainable data analysis with Snakemake785 cited

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  • 2021Replicability, Robustness, and Reproducibility in Psychological Science769 cited
  • Cited by

    • 2024ENCORE: a practical implementation to improve reproducibility and transparency of computational research11 cited
    • 2024Characterising reproducibility debt in scientific software: A systematic literature review9 cited
    • 2025Molecular biology in the exabyte era: Taming the data deluge for biological revelation and clinical transformation9 cited
    • 2024Detailed Implementation of a Reproducible Machine Learning-Enabled Workflow8 cited
    • 2025Study Area Map Generator: A Web-Based Shiny Application for Generating Country-Level Study Area Maps for Scientific Publications4 cited