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A terminology for scientific workflow systems
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A terminology for scientific workflow systems (2025)A terminology for scientific workflow sys…Applying the FAIR Principles to computational workflows (2025)Applying the FAIR Principles …Methods included (2022)Methods includedSustainable data analysis with Snakemake (2021)Sustainable data analysis wit…The nf-core framework for community-curated bioinformatics pipelines (2020)The nf-core framework for com…StreamFlow: Cross-Breeding Cloud With HPC (2020)StreamFlow: Cross-Breeding Cl…AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance (2020)AiiDA 1.0, a scalable computa…Workflow Automation for Cycling Systems (2019)Workflow Automation for Cycli…Toil enables reproducible, open source, big biomedical data analyses (2017)Toil enables reproducible, op…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…A characterization of workflow management systems for extreme-scale applications (2017)A characterization of workflo…FireWorks: a dynamic workflow system designed for high‐throughput applications (2015)FireWorks: a dynamic workflow…Dissemination of scientific software with Galaxy ToolShed (2014)Dissemination of scientific s…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…Towards a Taxonomy of Provenance in Scientific Workflow Management Systems (2009)Towards a Taxonomy of Provena…Workflows and e-Science: An overview of workflow system features and capabilities (2008)Workflows and e-Science: An o…Report from the NSF workshop on workflow and process automation in information systems (1996)Report from the NSF workshop …Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Scientific workflow management and the Kepler system (2005)pyiron: An integrated development environment for computational materials science (2019)Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows (2020)Next-generation sequencing data interpretation: enhancing reproducibility and accessibility (2012)Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud (2015)Practical Computational Reproducibility in the Life Sciences (2017)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)Design Patterns: Elements of Reusable Object-Oriented Software (1994)Bioconductor: open software development for computational biology and bioinformatics (2004)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Snakemake—a scalable bioinformatics workflow engine (2012)Reproducibility: A tragedy of errors (2016)Sustainable data analysis with Snakemake (2021)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)DolphinNext: a distributed data processing platform for high throughput genomics (2020)An AI Agent for Fully Automated Multi‐Omic Analyses (2024)Reproducible Research in Computational Science (2011)AiiDA: automated interactive infrastructure and database for computational science (2015)Materials Cloud, a platform for open computational science (2020)A dynamic knowledge graph approach to distributed self-driving laboratories (2024)KNIME - the Konstanz information miner (2009)A Community Roadmap for Scientific Workflows Research and Development (2021)The five pillars of computational reproducibility: bioinformatics and beyond (2023)Geospatial Cyberinfrastructure: Past, present and future (2010)Reproducibility in Scientific Computing (2018)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)
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References

  • 2020The nf-core framework for community-curated bioinformatics pipelines4,089 cited
  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2010Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences3,455 cited
  • 2017Toil enables reproducible, open source, big biomedical data analyses1,362 cited
  • 2008Workflows and e-Science: An overview of workflow system features and capabilities832 cited
  • 2021Sustainable data analysis with Snakemake785 cited
  • 2015FireWorks: a dynamic workflow system designed for high‐throughput applications548 cited
  • 2020AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance345 cited
  • 2014Dissemination of scientific software with Galaxy ToolShed257 cited
  • 2022Methods included182 cited
  • 2017A characterization of workflow management systems for extreme-scale applications149 cited
  • 2009Towards a Taxonomy of Provenance in Scientific Workflow Management Systems112 cited
  • 1996Report from the NSF workshop on workflow and process automation in information systems103 cited
  • 2020StreamFlow: Cross-Breeding Cloud With HPC88 cited
  • 2025

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Applying the FAIR Principles to computational workflows
75 cited
  • 2019Workflow Automation for Cycling Systems68 cited
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