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A Practical Guide to Reproducible Modeling for Biochemical Networks
16 references·0 citing·37 second hop
A Practical Guide to Reproducible Modeling for Biochemical Networks (2023)A Practical Guide to Reproducible Modelin…Reproducibility in systems biology modelling (2021)Reproducibility in systems bi…Improving reproducibility in computational biology research (2020)Improving reproducibility in …Best Practices for Making Reproducible Biochemical Models (2020)Best Practices for Making Rep…Ten simple rules on how to create open access and reproducible molecular simulations of biological systems (2019)Ten simple rules on how to cr…How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine (2016)How Modeling Standards, Softw…SEEK: a systems biology data and model management platform (2015)SEEK: a systems biology data …COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project (2014)COMBINE archive and OMEX form…Ten Simple Rules for Reproducible Computational Research (2013)Ten Simple Rules for Reproduc…BioServices: a common Python package to access biological Web Services programmatically (2013)BioServices: a common Python …Reproducible Research in Computational Science (2011)Reproducible Research in Comp…Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language (2011)Reproducible computational bi…Open science is a research accelerator (2011)Open science is a research ac…Believe it or not: how much can we rely on published data on potential drug targets? (2011)Believe it or not: how much c…Reproducible Science (2010)Reproducible ScienceBasics of estimating measurement uncertainty. (2008)Basics of estimating measurem…Software for Portable Scientific Data Management (1993)Software for Portable Scienti…openBIS: a flexible framework for managing and analyzing complex data in biology research (2011)An overview of the model integration process: From pre-integration assessment to testing (2016)WorkflowHub: a registry for computational workflows (2025)The Gift Relationship: From Human Blood to Social Policy. (1972)The gift relationship from human blood to social policy (1997)The Blue Obelisk—Interoperability in Chemical Informatics (2006)Human-Data Interaction: The Human Face of the Data-Driven Society (2014)Position paper: Open web-distributed integrated geographic modelling and simulation to enable broader participation and applications (2020)The Open Innovation in Science research field: a collaborative conceptualisation approach (2020)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)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)Why Most Published Research Findings Are False (2005)The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta‐analyses (2016)Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015 (2018)A standard protocol for describing individual-based and agent-based models (2006)Accessible Reproducible Research (2010)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)BioCatalogue: a universal catalogue of web services for the life sciences (2010)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)Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows (2022)Wonderful life: the Burgess Shale and the nature of history (1990)The black swan: the impact of the highly improbable (2007)On the scientific superiority of conceptual replications for scientific progress (2016)Reproducibility in Computational Neuroscience Models and Simulations (2016)Open science, communal culture, and women’s participation in the movement to improve science (2020)Increasing value and reducing waste in research design, conduct, and analysis (2014)Reproducibility in Science (2014)An introduction to Docker for reproducible research (2015)
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References

  • 2011Believe it or not: how much can we rely on published data on potential drug targets?1,885 cited
  • 2011Reproducible Research in Computational Science1,446 cited
  • 2013Ten Simple Rules for Reproducible Computational Research875 cited
  • 2011Open science is a research accelerator260 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
  • 2013BioServices: a common Python package to access biological Web Services programmatically128 cited
  • 2010Reproducible Science124 cited
  • 2015SEEK: a systems biology data and model management platform113 cited
  • 2008Basics of estimating measurement uncertainty.78 cited
  • 1993Software for Portable Scientific Data Management56 cited
  • 2016How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine49 cited
  • 2020Best Practices for Making Reproducible Biochemical Models45 cited
  • 2019Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

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  • 2020Improving reproducibility in computational biology research42 cited
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