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Recent advances in biomedical simulations: a manifesto for model engineering
8 references·2 citing·34 second hop
Recent advances in biomedical simulations: a manifesto for model engineering (2019)Recent advances in biomedical simulations…The Practice of Reproducible Research (2019)The Practice of Reproducible …Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology (2018)Tellurium notebooks—An enviro…Sciunits: Reusable Research Objects (2017)Sciunits: Reusable Research O…Reproducibility in Computational Neuroscience Models and Simulations (2016)Reproducibility in Computatio…1,500 scientists lift the lid on reproducibility (2016)1,500 scientists lift the lid…The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication. (2014)The Jupyter/IPython architect…Ten Simple Rules for Reproducible Computational Research (2013)Ten Simple Rules for Reproduc…Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language (2011)Reproducible computational bi…Standards, dissemination, and best practices in systems biology (2023)Standards, dissemination, and…Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology (2021)Practical resources for enhan…Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Galaxy: A platform for interactive large-scale genome analysis (2005)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Reproducibility in Science (2014)Good enough practices in scientific computing. (2017)Preferred reporting items for systematic reviews and meta‐analyses in ecology and evolutionary biology: a PRISMA extension (2021)Conjectures and Refutations: The Growth of Scientific Knowledge. (1964)Working Memory (1992)The CellML Model Repository (2008)Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience (2018)Evolution and Reproducibility of Simulation Modeling in Epidemiology and Health Policy Over Half a Century (2021)Provenance Collection Support in the Kepler Scientific Workflow System (2006)Implementing Reproducible Research (2014)Integrating scientific cyberinfrastructures to improve reproducibility in computational hydrology: Example for HydroShare and GeoTrust (2018)Utilizing Provenance in Reusable Research Objects (2018)A taxonomy for reproducible and replicable research in environmental modelling (2020)Believe it or not: how much can we rely on published data on potential drug targets? (2011)“Reproducible” Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach (2018)Publishing reproducible dynamic kinetic models (2020)BioContainers: an open-source and community-driven framework for software standardization (2017)Publish or impoverish (2017)Characterising reproducibility debt in scientific software: A systematic literature review (2024)What does research reproducibility mean? (2016)Towards FAIR principles for research software (2019)Reproducibility standards for machine learning in the life sciences (2021)COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project (2014)Proceedings of the 2017 Winter Simulation Conference (2017)Reproducibility in systems biology modelling (2021)A manifesto for reproducible science (2017)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)The nf-core framework for community-curated bioinformatics pipelines (2020)Methods for enhancing the reproducibility of biomedical research findings using electronic health records (2017)The GenePattern Notebook Environment (2017)Solar radiation modeling with KNIME and Solar Analyst: Increasing environmental model reproducibility using scientific workflows (2020)
this work references cited by second hop

References

  • 20161,500 scientists lift the lid on reproducibility4,200 cited
  • 2013Ten Simple Rules for Reproducible Computational Research875 cited
  • 2011Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language257 cited
  • 2014The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication.79 cited
  • 2016Reproducibility in Computational Neuroscience Models and Simulations70 cited
  • 2018Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology55 cited
  • 2017Sciunits: Reusable Research Objects54 cited
  • 2019The Practice of Reproducible Research40 cited

Cited by

  • 2023Standards, dissemination, and best practices in systems biology15 cited
  • 2021Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology14 cited

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