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"modifiers<-", "modifiers<-,Reaction-method", "name,Reaction-method", "name<-,Reaction-method", "products", "products,Reaction-method", "products<-", "products<-,Reaction-method", "reactants", "reactants,Reaction-method", "reactants<-", "reactants<-,Reaction-method", "Reaction-class", "reversible", "reversible,Reaction-method", "reversible<-", "reversible<-,Reaction-method" ] }, { "page": "ReactionGlyph-class", "title": "SBML type \"ReactionGlyph\"", "topics": [ "glyphCurve", "glyphCurve,ReactionGlyph-method", "glyphCurve<-", "glyphCurve<-,ReactionGlyph-method", "reaction", "reaction,ReactionGlyph-method", "reaction<-", "reaction<-,ReactionGlyph-method", "ReactionGlyph-class", "speciesReferenceGlyphs", "speciesReferenceGlyphs,ReactionGlyph-method", "speciesReferenceGlyphs<-", "speciesReferenceGlyphs<-,ReactionGlyph-method" ] }, { "page": "Rule-class", "title": "SBML type \"Rule\"", "topics": [ "math,Rule-method", "math<-,Rule-method", "Rule-class" ] }, { "page": "SBase-class", "title": "SBML type \"SBase\"", "topics": [ "annotation", "annotation,SBase-method", "annotation<-", "annotation<-,SBase-method", "cvTerms", "cvTerms,SBase-method", "cvTerms<-", "cvTerms<-,SBase-method", "metaId", "metaId,SBase-method", "metaId<-", "metaId<-,SBase-method", "notes", "notes,SBase-method", "notes<-", "notes<-,SBase-method", "SBase-class", "sboTerm", "sboTerm,SBase-method", "sboTerm<-", "sboTerm<-,SBase-method" ] }, { "page": "read", "title": "Read in an SBML file (start here)", "topics": [ "rsbml_read" ] }, { "page": "SBML-class", "title": "SBML type \"SBML\"", "topics": [ "as.character.SBML", "coerce", "coerce,SBML,graph-method", "coerce,SBML,SBMLDocument-method", "level", "level,SBML-method", "level<-", "level<-,SBML-method", "model", "model,SBML-method", "model<-", "model<-,SBML-method", "rsbml_check,SBML-method", "rsbml_doc", "rsbml_doc,SBML-method", "rsbml_graph,SBML-method", "rsbml_write", "rsbml_write,SBML-method", "rsbml_xml", "rsbml_xml,SBML-method", "SBML-class", "simulate,SBML-method", "ver", "ver,SBML-method", "ver<-", "ver<-,SBML-method" ] }, { "page": "SBMLDocument-class", "title": "\"SBMLDocument\" from libsbml", "topics": [ "as.character.SBMLDocument", "coerce,SBMLDocument,graph-method", "coerce,SBMLDocument,SBML-method", "rsbml_check", "rsbml_check,SBMLDocument-method", "rsbml_dom", "rsbml_dom,SBMLDocument-method", "rsbml_graph", "rsbml_graph,Model-method", "rsbml_graph,SBMLDocument-method", "rsbml_problems", "rsbml_problems,SBMLDocument-method", "rsbml_write,SBMLDocument-method", "rsbml_xml,SBMLDocument-method", "SBMLDocument-class", "simulate,SBMLDocument-method" ] }, { "page": "SBMLProblem-class", "title": "SBMLProblem", "topics": [ ".condition,SBMLProblem-method", ".throw,SBMLError-method", ".throw,SBMLFatal-method", ".throw,SBMLInfo-method", ".throw,SBMLWarning-method", "SBMLError-class", "SBMLFatal-class", "SBMLInfo-class", "SBMLProblem-class", "SBMLWarning-class", "show,SBMLProblem-method" ] }, { "page": "SBMLProblems-class", "title": "SBMLProblems", "topics": [ ".throw,SBMLProblems-method", "errors", "errors,SBMLProblems-method", "fatals", "fatals,SBMLProblems-method", "infos", "infos,SBMLProblems-method", "SBMLProblems-class", "warns", "warns,SBMLProblems-method" ] }, { "page": "SimpleSpeciesReference-class", "title": "SBML type \"SimpleSpeciesReference\"", "topics": [ "id,SimpleSpeciesReference-method", "id<-,SimpleSpeciesReference-method", "SimpleSpeciesReference-class", "species,SimpleSpeciesReference-method", "species<-,SimpleSpeciesReference-method" ] }, { "page": "SOSDesign-class", "title": "SOSDesign", "topics": [ "reactions,SOSDesign-method", "reactions<-,SOSDesign-method", "SOSDesign-class" ] }, { "page": "SOSExperiment-class", "title": "SOS Experiment", "topics": [ "simulate", "simulate,SOSExperiment-method", "SOSExperiment-class" ] }, { "page": "SOSProtocol-class", "title": "SOSProtocol", "topics": [ "SOSProtocol-class" ] }, { "page": "SOSResult-class", "title": "SOSResult", "topics": [ "as.ts,SOSResult-method", "compartments,SOSResult-method", "parameters,SOSResult-method", "reactions,SOSResult-method", "SOSResult-class", "species,SOSResult-method" ] }, { "page": "SOSSubject-class", "title": "SOSSubject", "topics": [ "SOSSubject-class" ] }, { "page": "Species-class", "title": "SBML type \"Species\"", "topics": [ "boundaryCondition", "boundaryCondition,Species-method", "boundaryCondition<-", "boundaryCondition<-,Species-method", "charge", "charge,Species-method", "charge<-", "charge<-,Species-method", "compartment", "compartment,Species-method", "compartment<-", "compartment<-,Species-method", "constant", "constant,Species-method", "constant<-", "constant<-,Species-method", "hasOnlySubstanceUnits", "hasOnlySubstanceUnits,Species-method", "hasOnlySubstanceUnits<-", "hasOnlySubstanceUnits<-,Species-method", "id,Species-method", "id<-,Species-method", "initialAmount", "initialAmount,Species-method", "initialAmount<-", "initialAmount<-,Species-method", "initialConcentration", "initialConcentration,Species-method", "initialConcentration<-", "initialConcentration<-,Species-method", "name,Species-method", "name<-,Species-method", "spatialSizeUnits", "spatialSizeUnits,Species-method", "spatialSizeUnits<-", "spatialSizeUnits<-,Species-method", "Species-class", "substanceUnits,Species-method", "substanceUnits<-,Species-method", "units,Species-method", "units<-,Species-method" ] }, { "page": "SpeciesConcentrationRule-class", "title": "SBML type \"SpeciesConcentrationRule\"", "topics": [ "species,SpeciesConcentrationRule-method", "species<-,SpeciesConcentrationRule-method", "SpeciesConcentrationRule-class" ] }, { "page": "SpeciesGlyph-class", "title": "SBML type \"SpeciesGlyph\"", "topics": [ "species", "species,SpeciesGlyph-method", "species<-", "species<-,SpeciesGlyph-method", "SpeciesGlyph-class" ] }, { "page": "SpeciesReference-class", "title": "SBML type \"SpeciesReference\"", "topics": [ "SpeciesReference-class", "stoichiometry", "stoichiometry,SpeciesReference-method", "stoichiometry<-", "stoichiometry<-,SpeciesReference-method", "stoichiometryMath", "stoichiometryMath,SpeciesReference-method", "stoichiometryMath<-", "stoichiometryMath<-,SpeciesReference-method" ] }, { "page": "SpeciesReferenceGlyph-class", "title": "SBML type \"SpeciesReferenceGlyph\"", "topics": [ "glyphCurve,SpeciesReferenceGlyph-method", "glyphCurve<-,SpeciesReferenceGlyph-method", "role", "role,SpeciesReferenceGlyph-method", "role<-", "role<-,SpeciesReferenceGlyph-method", "speciesGlyph", "speciesGlyph,SpeciesReferenceGlyph-method", "speciesGlyph<-", "speciesGlyph<-,SpeciesReferenceGlyph-method", "speciesReference", "speciesReference,SpeciesReferenceGlyph-method", "speciesReference<-", "speciesReference<-,SpeciesReferenceGlyph-method", "SpeciesReferenceGlyph-class" ] }, { "page": "SpeciesType-class", "title": "SBML Type \"SpeciesType\"", "topics": [ "id,SpeciesType-method", "id<-,SpeciesType-method", "name,SpeciesType-method", "name<-,SpeciesType-method", "SpeciesType-class" ] }, { "page": "StoichiometryMath-class", "title": "SBML type \"StoichiometryMath\"", "topics": [ "math,StoichiometryMath-method", "math<-,StoichiometryMath-method", "OptionalStoichiometryMath-class", "StoichiometryMath-class" ] }, { "page": "TextGlyph-class", "title": "SBML type \"TextGlyph\"", "topics": [ "graphicalObject", "graphicalObject,TextGlyph-method", "graphicalObject<-", "graphicalObject<-,TextGlyph-method", "originOfText", "originOfText,TextGlyph-method", "originOfText<-", "originOfText<-,TextGlyph-method", "text", "text,TextGlyph-method", "text<-", "text<-,TextGlyph-method", "TextGlyph-class" ] }, { "page": "Trigger-class", "title": "SBML Type \"Trigger\"", "topics": [ "math,Trigger-method", "math<-,Trigger-method", "Trigger-class" ] }, { "page": "Unit-class", "title": "SBML type \"Unit\"", "topics": [ "exponent", "exponent,Unit-method", "exponent<-", "exponent<-,Unit-method", "kind", "kind,Unit-method", "kind<-", 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