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Specifications of standards in systems and synthetic biology: status and developments in 2021
13 references·0 citing·27 second hop
Specifications of standards in systems and synthetic biology: status and developments in 2021 (2021)Specifications of standards in systems an…The simulation experiment description markup language (SED-ML): language specification for level 1 version 4 (2021)The simulation experiment des…OMEX metadata specification (version 1.2) (2021)OMEX metadata specification (…The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) (2020)The first 10 years of the int…Open modeling and exchange (OMEX) metadata specification version 1.0 (2020)Open modeling and exchange (O…CellML 2.0 (2020)CellML 2.0A brief history of COMBINE (2017)A brief history of COMBINEThe CellML Metadata Framework 2.0 Specification (2015)The CellML Metadata Framework…Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative (2015)Promoting Coordinated Develop…COMBINE Archive Specification Version 1 (2015)COMBINE Archive Specification…Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) (2014)Meeting report from the fourt…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…BioModels.net Web Services, a free and integrated toolkit for computational modelling software (2009)BioModels.net Web Services, a…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)Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Model storage, exchange and integration (2006)ERROR ANALYSIS AND PROPAGATION IN METABOLOMICS DATA ANALYSIS (2013)Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models (2016)SED-ML – An XML Format for the Implementation of the MIASE Guidelines (2008)The Physiome Model Repository 2 (2011)The CombineArchiveWeb application – A web based tool to handle files associated with modelling results (2014)Combining computational models, semantic annotations and simulation experiments in a graph database (2015)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)BioModels—15 years of sharing computational models in life science (2019)Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways (2022)Bayesian estimation reveals that reproducible models in Systems Biology get more citations (2023)Minimum Information About a Simulation Experiment (MIASE) (2011)ENCORE: a practical implementation to improve reproducibility and transparency of computational research (2024)The simulation experiment description markup language (SED-ML): language specification for level 1 version 5 (2024)Reproducibility in systems biology modelling (2021)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)RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats (2021)Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology (2022)BioSimulators : a central registry of simulation engines and services for recommending specific tools (2022)
this work references cited by second hop

References

  • 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
  • 2015Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative116 cited
  • 2009BioModels.net Web Services, a free and integrated toolkit for computational modelling software51 cited
  • 2020CellML 2.042 cited
  • 2020The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)38 cited
  • 2014Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)29 cited
  • 2021The simulation experiment description markup language (SED-ML): language specification for level 1 version 417 cited
  • 2015The CellML Metadata Framework 2.0 Specification15 cited
  • 2020Open modeling and exchange (OMEX) metadata specification version 1.012 cited
  • 2021OMEX metadata specification (version 1.2)11 cited
  • 2017A brief history of COMBINE10 cited
  • 2015COMBINE Archive Specification Version 18 cited

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