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Bioimage analysis workflows: community resources to navigate through a complex ecosystem
16 references·2 citing·34 second hop
Bioimage analysis workflows: community resources to navigate through a complex ecosystem (2021)Bioimage analysis workflows: community re…Sustainable data analysis with Snakemake (2021)Sustainable data analysis wit…Sustainable data analysis with Snakemake (2021)Sustainable data analysis wit…Reproducible image handling and analysis (2021)Reproducible image handling a…The nf-core framework for community-curated bioinformatics pipelines (2020)The nf-core framework for com…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update (2020)The Galaxy platform for acces…The bio.tools registry of software tools and data resources for the life sciences (2019)The bio.tools registry of sof…Recommendations for the packaging and containerizing of bioinformatics software (2019)Recommendations for the packa…FAIR Computational Workflows (2019)FAIR Computational WorkflowsRecommendations for the packaging and containerizing of bioinformatics software (2018)Recommendations for the packa…BioContainers: an open-source and community-driven framework for software standardization (2017)BioContainers: an open-source…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…Common Workflow Language, draft 3 (2016)Common Workflow Language, dra…A review of bioinformatic pipeline frameworks (2016)A review of bioinformatic pip…Tools and data services registry: a community effort to document bioinformatics resources (2015)Tools and data services regis…ITK: enabling reproducible research and open science (2014)ITK: enabling reproducible re…KNIME - the Konstanz information miner (2009)KNIME - the Konstanz informat…Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice (2023)Building Domain-Specific Mach…Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks (2022)Cloud-enabled Biodepot workfl…The Logic of Scientific Discovery. (1959)The Structure of Scientific Revolutions (1963)The Logic of Scientific Discovery (2013)Co-creación e innovación abierta : Revisión sistemática de literatura (2017)Co-creation and open innovation: Systematic literature review (2017)The academic impact of Open Science: a scoping review (2025)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Snakemake—a scalable bioinformatics workflow engine (2012)The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)snakePipes: facilitating flexible, scalable and integrative epigenomic analysis (2019)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Galaxy: A platform for interactive large-scale genome analysis (2005)What does research reproducibility mean? (2016)1,500 scientists lift the lid on reproducibility (2016)Nextflow enables reproducible computational workflows (2017)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)DolphinNext: a distributed data processing platform for high throughput genomics (2020)An AI Agent for Fully Automated Multi‐Omic Analyses (2024)Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)Singularity: Scientific containers for mobility of compute (2017)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (2022)Empowering bioinformatics communities with Nextflow and nf-core (2025)Blending Big Data Analytics: Review on Challenges and a Recent Study (2019)Towards reproducible computational drug discovery (2020)Methods included (2022)Towards FAIR principles for research software (2019)The five pillars of computational reproducibility: bioinformatics and beyond (2023)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)Applying the FAIR Principles to computational workflows (2025)Practical Computational Reproducibility in the Life Sciences (2017)Scientific workflows: Past, present and future (2017)BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows (2019)
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References

  • 2020The nf-core framework for community-curated bioinformatics pipelines4,089 cited
  • 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update2,149 cited
  • 2021Sustainable data analysis with Snakemake1,646 cited
  • 2009KNIME - the Konstanz information miner1,190 cited
  • 2017BioContainers: an open-source and community-driven framework for software standardization798 cited
  • 2021Sustainable data analysis with Snakemake785 cited
  • 2020The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update522 cited
  • 2014ITK: enabling reproducible research and open science377 cited
  • 2016A review of bioinformatic pipeline frameworks250 cited
  • 2016Common Workflow Language, draft 3204 cited
  • 2019FAIR Computational Workflows171 cited
  • 2015Tools and data services registry: a community effort to document bioinformatics resources153 cited
  • 2019The bio.tools registry of software tools and data resources for the life sciences88 cited
  • 2021Reproducible image handling and analysis61 cited
  • 2019Recommendations for the packaging and containerizing of bioinformatics software50 cited

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  • 2018Recommendations for the packaging and containerizing of bioinformatics software38 cited
  • Cited by

    • 2022Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks10 cited
    • 2023Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice10 cited