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Evaluating Tools for Enhancing Reproducibility in Computational Scientific Experiments
16 references·0 citing·42 second hop
Evaluating Tools for Enhancing Reproducibility in Computational Scientific Experiments (2024)Evaluating Tools for Enhancing Reproducib…The fundamental principles of reproducibility (2021)The fundamental principles of…Reproducibility and Replicability in Science (2019)Reproducibility and Replicabi…Reproducibility in Scientific Computing (2018)Reproducibility in Scientific…Computing environments for reproducibility: Capturing the “Whole Tale” (2018)Computing environments for re…Binder 2.0 - Reproducible, interactive, sharable environments for science at scale (2018)Binder 2.0 - Reproducible, in…The Popper Convention: Making Reproducible Systems Evaluation Practical (2017)The Popper Convention: Making…Sciunits: Reusable Research Objects (2017)Sciunits: Reusable Research O…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts (2015)YesWorkflow: A User-Oriented,…ResearchCompendia.org: Cyberinfrastructure for Reproducibility and Collaboration in Computational Science (2015)ResearchCompendia.org: Cyberi…COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project (2014)COMBINE archive and OMEX form…CARE, the comprehensive archiver for reproducible execution (2014)CARE, the comprehensive archi…Making Computations and Publications Reproducible with VisTrails (2012)Making Computations and Publi…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…Scientific workflow management and the Kepler system (2005)Scientific workflow managemen…WaveLab and Reproducible Research (1995)WaveLab and Reproducible Rese…Bioconductor: open software development for computational biology and bioinformatics (2004)noWorkflow (2017)Vamsa: Automated Provenance Tracking in Data Science Scripts (2020)Outlining Traceability: A Principle for Operationalizing Accountability in Computing Systems (2021)Workflow Management (2002)Workflow Patterns (2003)Taverna: lessons in creating a workflow environment for the life sciences (2005)Provenance and scientific workflows (2008)FireWorks: a dynamic workflow system designed for high‐throughput applications (2015)A standard protocol for describing individual-based and agent-based models (2006)Accessible Reproducible Research (2010)Ten Simple Rules for Reproducible Computational Research (2013)Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative (2015)Proceedings of the 2017 Winter Simulation Conference (2017)Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology (2018)Design Patterns: Elements of Reusable Object-Oriented Software (1994)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)The nf-core framework for community-curated bioinformatics pipelines (2020)Sustainable data analysis with Snakemake (2021)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)Promoting an open research culture (2015)Reproducibility and replicability: opportunities and challenges for geospatial research (2020)Ten simple rules for writing Dockerfiles for reproducible data science (2020)Traceability for Trustworthy AI: A Review of Models and Tools (2021)Why Most Published Research Findings Are False (2005)Why Most Published Research Findings Are False (2005)The Logic of Scientific Discovery (2013)Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (2019)A taxonomy for reproducible and replicable research in environmental modelling (2020)The data science life cycle (2020)Statistical Analyses and Reproducible Research (2007)1,500 scientists lift the lid on reproducibility (2016)Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks (2019)Using Jupyter for Reproducible Scientific Workflows (2021)A large-scale study on research code quality and execution (2022)Scientific Utopia (2012)Recommendations for Increasing Replicability in Psychology (2013)Challenges for assessing replicability in preclinical cancer biology (2021)Replicability, Robustness, and Reproducibility in Psychological Science (2021)Prevalence of questionable research practices, research misconduct and their potential explanatory factors: A survey among academic researchers in The Netherlands (2022)
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References

  • 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
  • 2005Scientific workflow management and the Kepler system1,681 cited
  • 2019Reproducibility and Replicability in Science921 cited
  • 1995WaveLab and Reproducible Research543 cited
  • 2018Binder 2.0 - Reproducible, interactive, sharable environments for science at scale302 cited
  • 2014COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project170 cited
  • 2018Reproducibility in Scientific Computing149 cited
  • 2018Computing environments for reproducibility: Capturing the “Whole Tale”132 cited
  • 2015YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts103 cited
  • 2021The fundamental principles of reproducibility92 cited
  • 2012Making Computations and Publications Reproducible with VisTrails65 cited
  • 2017The Popper Convention: Making Reproducible Systems Evaluation Practical60 cited
  • 2017Sciunits: Reusable Research Objects54 cited
  • 2014CARE, the comprehensive archiver for reproducible execution

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37 cited
  • 2015ResearchCompendia.org: Cyberinfrastructure for Reproducibility and Collaboration in Computational Science31 cited
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