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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
7 references·1 citing·25 second hop
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology (2022)Addressing barriers in comprehensiveness,…Reproducibility in systems biology modelling (2021)Reproducibility in systems bi…Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective (2020)Credible practice of modeling…CellML 2.0 (2020)CellML 2.0BioModels—15 years of sharing computational models in life science (2019)BioModels—15 years of sharing…Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative (2015)Promoting Coordinated Develop…COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project (2014)COMBINE archive and OMEX form…Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language (2011)Reproducible computational bi…Making PBPK models more reproducible in practice (2024)Making PBPK models more repro…A standard protocol for describing individual-based and agent-based models (2006)Accessible Reproducible Research (2010)Ten Simple Rules for Reproducible Computational Research (2013)Proceedings of the 2017 Winter Simulation Conference (2017)Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology (2018)The Physiome Model Repository 2 (2011)OpenCOR: a modular and interoperable approach to computational biology (2015)How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine (2016)Reproducibility in Computational Neuroscience Models and Simulations (2016)Simulation Modeling and Analysis. (1983)Sensitivity Analysis for Importance Assessment (2002)Verification and Validation in Scientific Computing (2010)Computational models in systems biology: standards, dissemination, and best practices (2022)Methods That Support the Validation of Agent-Based Models: An Overview and Discussion (2024)Toward Good Simulation Practice (2024)1,500 scientists lift the lid on reproducibility (2016)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)Reproducibility vs. Replicability: A Brief History of a Confused Terminology (2018)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)RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats (2021)BioSimulators : a central registry of simulation engines and services for recommending specific tools (2022)
this work references cited by second hop

References

  • 2019BioModels—15 years of sharing computational models in life science361 cited
  • 2011Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language257 cited
  • 2014COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project170 cited
  • 2021Reproducibility in systems biology modelling131 cited
  • 2020Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective118 cited
  • 2015Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative116 cited
  • 2020CellML 2.042 cited

Cited by

  • 2024Making PBPK models more reproducible in practice12 cited

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