about
Annotation-based feature extraction from sets of SBML modelsMinimum Information About a Simulation Experiment (MIASE)Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup LanguagePromoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE InitiativeSTON: exploring biological pathways using the SBGN standard and graph databasesCombining computational models, semantic annotations and simulation experiments in a graph databaseMeeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)Controlled vocabularies and semantics in systems biologyRanked retrieval of Computational Biology modelsToward Community Standards and Software for Whole-Cell ModelingSystems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model DefinitionsAn algorithm to detect and communicate the differences in computational models describing biological systems.A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryosCOMODI: an ontology to characterise differences in versions of computational models in biologyA call for virtual experiments: accelerating the scientific process.Specifications of Standards in Systems and Synthetic Biology.Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.Improving the reuse of computational models through version control.Notions of similarity for systems biology models.The JWS online simulation database.Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.Specifications of Standards in Systems and Synthetic Biology.Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).Evolution of computational models in BioModels Database and the Physiome Model Repository.The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.SED-ML web tools: generate, modify and export standard-compliant simulation studies.Notions of similarity for systems biology models.The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 CoreSBML Level 3 Package Proposal: AnnotationHarmonizing semantic annotations for computational models in biologyKinetic Simulation Algorithm OntologySED-ML Web Tools: Generate, modify and export standard-compliant simulation studiesSED-ML Web Tools: Generate, modify and export standard-compliant simulation studiesA brief history of COMBINESystems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model DefinitionsIdentifying frequent patterns in biochemical reaction networks - a workflowIdentifying frequent patterns in biochemical reaction networks - a workflowIdentifying frequent patterns in biochemical reaction networks - a workflow
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Dagmar Waltemath
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