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From FAIR to CURE: guidelines for computational models of biological systems
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From FAIR to CURE: guidelines for computational models of biological systems (2026)From FAIR to CURE: guidelines for computa…Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology (2022)Addressing barriers in compre…Reproducibility in systems biology modelling (2021)Reproducibility in systems bi…Theories and Models: What They Are, What They Are for, and What They Are About (2020)Theories and Models: What The…Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective (2020)Credible practice of modeling…CellML 2.0 (2020)CellML 2.0Best Practices for Making Reproducible Biochemical Models (2020)Best Practices for Making Rep…Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology (2018)Tellurium notebooks—An enviro…Reproducibility vs. Replicability: A Brief History of a Confused Terminology (2018)Reproducibility vs. Replicabi…KBase: The United States Department of Energy Systems Biology Knowledgebase (2018)KBase: The United States Depa…The JWS online simulation database (2017)The JWS online simulation dat…How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine (2016)How Modeling Standards, Softw…1,500 scientists lift the lid on reproducibility (2016)1,500 scientists lift the lid…FieldML, a proposed open standard for the Physiome project for mathematical model representation (2013)FieldML, a proposed open stan…An evolution of uncertainty assessment and quantification (2011)An evolution of uncertainty a…Model storage, exchange and integration (2006)Model storage, exchange and i…Terminology for model credibility (1979)Terminology for model credibi…Why Most Published Research Findings Are False (2005)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)The Logic of Scientific Discovery (2013)Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities (2019)Ten simple rules on how to create open access and reproducible molecular simulations of biological systems (2019)Reproducible Research in Computational Science (2011)Journal of Computational Neuroscience (2013)What does research reproducibility mean? (2016)Open science, reproducibility, and transparency in ecology (2018)Reproducibility in machine learning for health research: Still a ways to go (2021)Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)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)Recent advances in biomedical simulations: a manifesto for model engineering (2019)Publishing reproducible dynamic kinetic models (2020)Positioning and Power in Academic Publishing: Players, Agents and Agendas (2016)Navigating the maze: the impact of configurability in bioinformatics software (2018)Situating Ecology as a Big-Data Science: Current Advances, Challenges, and Solutions (2018)Advancing Equity and Inclusion in Microbiome Research and Training (2021)Simulation Modeling and Analysis. (1983)Sensitivity Analysis for Importance Assessment (2002)Verification and Validation in Scientific Computing (2010)Methods That Support the Validation of Agent-Based Models: An Overview and Discussion (2024)Toward Good Simulation Practice (2024)Collected Papers of Charles Sanders Peirce (1935)Theoretical risks and tabular asterisks: Sir Karl, Sir Ronald, and the slow progress of soft psychology. (1978)Choosing Prediction Over Explanation in Psychology: Lessons From Machine Learning (2017)Intervening on psychopathology networks: Evaluating intervention targets through simulations (2021)A manifesto for applying behavioural science (2023)Current interpretations of the I-PACE model of behavioral addictions (2025)A manifesto for reproducible science (2017)To Sobol or not to Sobol? The effects of sampling schemes in systems biology applications (2021)BioUML—towards a universal research platform (2022)Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows (2022)BioModels.net Web Services, a free and integrated toolkit for computational modelling software (2009)A-R-E: The Author-Review-Execute Environment (2011)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)The nf-core framework for community-curated bioinformatics pipelines (2020)Validation, verification, and testing techniques throughout the life cycle of a simulation study (1994)Verification and Validation of Simulation Models (2006)Verification and validation of simulation models (2010)
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References

  • 20161,500 scientists lift the lid on reproducibility4,200 cited
  • 2018KBase: The United States Department of Energy Systems Biology Knowledgebase1,620 cited
  • 2018Reproducibility vs. Replicability: A Brief History of a Confused Terminology426 cited
  • 1979Terminology for model credibility413 cited
  • 2020Theories and Models: What They Are, What They Are for, and What They Are About131 cited
  • 2021Reproducibility in systems biology modelling131 cited
  • 2020Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective118 cited
  • 2006Model storage, exchange and integration97 cited
  • 2018Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology55 cited
  • 2016How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine49 cited
  • 2011An evolution of uncertainty assessment and quantification46 cited
  • 2020Best Practices for Making Reproducible Biochemical Models45 cited
  • 2020CellML 2.042 cited
  • 2013FieldML, a proposed open standard for the Physiome project for mathematical model representation36 cited
  • 2017The JWS online simulation database

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  • 2022Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology32 cited
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