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Computational models in systems biology: standards, dissemination, and best practices
10 references·1 citing·36 second hop
Computational models in systems biology: standards, dissemination, and best practices (2022)Computational models in systems biology: …Reproducibility in systems biology modelling (2021)Reproducibility in systems bi…The ODD Protocol for Describing Agent-Based and Other Simulation Models: A Second Update to Improve Clarity, Replication, and Structural Realism (2020)The ODD Protocol for Describi…On code sharing and model documentation of published individual and agent-based models (2020)On code sharing and model doc…Improving reproducibility in computational biology research (2020)Improving reproducibility in …Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective (2020)Credible practice of modeling…BioModels—15 years of sharing computational models in life science (2019)BioModels—15 years of sharing…The Practice of Archiving Model Code of Agent-Based Models (2017)The Practice of Archiving Mod…1,500 scientists lift the lid on reproducibility (2016)1,500 scientists lift the lid…The ODD protocol: A review and first update (2010)The ODD protocol: A review an…A standard protocol for describing individual-based and agent-based models (2006)A standard protocol for descr…From FAIR to CURE: guidelines for computational models of biological systems (2026)From FAIR to CURE: guidelines…The Science of Scientific Writing (1990)Uses and Abuses of Mathematics in Biology (2004)Agent-Based Modeling of Energy Technology Adoption: Empirical Integration of Social, Behavioral, Economic, and Environmental Factors (2014)Everything you need to know about agent-based modelling and simulation (2016)Simulation as experiment: a philosophical reassessment for biological modeling (2004)A New Tool for Epidemiology: The Usefulness of Dynamic-Agent Models in Understanding Place Effects on Health (2008)Agent-based modeling in marketing: Guidelines for rigor (2011)Journals unite for reproducibility (2014)Repeatability in computer systems research (2016)The nlrx r package: A next‐generation framework for reproducible NetLogo model analyses (2019)Why Most Published Research Findings Are False (2005)Why Most Published Research Findings Are False (2005)Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology (2021)Advancing code sharing in the computational biology community (2022)ENCORE: a practical implementation to improve reproducibility and transparency of computational research (2024)Reproducible Research in Computational Science (2011)A meta-epidemiological assessment of transparency indicators of infectious disease models (2022)Pre-registration of mathematical models (2022)An analysis of the effects of sharing research data, code, and preprints on citations (2024)Simulation Modeling and Analysis. (1983)Sensitivity Analysis for Importance Assessment (2002)Verification and Validation in Scientific Computing (2010)Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology (2022)Methods That Support the Validation of Agent-Based Models: An Overview and Discussion (2024)Toward Good Simulation Practice (2024)What does research reproducibility mean? (2016)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)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)The nf-core framework for community-curated bioinformatics pipelines (2020)The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) (2020)Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows (2022)How to Translate a Verbal Theory Into a Formal Model (2020)Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach (2020)Agents.jl: a performant and feature-full agent-based modeling software of minimal code complexity (2022)
this work references cited by second hop

References

  • 20161,500 scientists lift the lid on reproducibility4,200 cited
  • 2006A standard protocol for describing individual-based and agent-based models2,985 cited
  • 2010The ODD protocol: A review and first update2,459 cited
  • 2020The ODD Protocol for Describing Agent-Based and Other Simulation Models: A Second Update to Improve Clarity, Replication, and Structural Realism899 cited
  • 2019BioModels—15 years of sharing computational models in life science361 cited
  • 2021Reproducibility in systems biology modelling131 cited
  • 2020Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective118 cited
  • 2020On code sharing and model documentation of published individual and agent-based models57 cited
  • 2020Improving reproducibility in computational biology research42 cited
  • 2017The Practice of Archiving Model Code of Agent-Based Models38 cited

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  • 2026From FAIR to CURE: guidelines for computational models of biological systems8 cited

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