rsbml: R support for SBML, using libsbml

Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.

AuthorMichael Lawrence <michafla@gene.com>
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseArtistic-2.0
Version2.32.0
http://www.sbml.org

View on Bioconductor

Man pages

AlgebraicRule-class: SBML type "AlgebraicRule"

AssignmentRule-class: SBML type "AssignmentRule"

BoundingBox-class: SBML type "BoundingBox"

Compartment-class: SBML type "Compartment"

CompartmentGlyph-class: SBML type "CompartmentGlyph"

CompartmentType-class: SBML Type "CompartmentType"

CompartmentVolumeRule-class: SBML type "CompartmentVolumeRule"

Constraint-class: SBML Type "Constraint"

CubicBezier-class: SBML type "CubicBezier"

Curve-class: SBML type "Curve"

CVTerm-class: SBML Type "CVTerm"

Delay-class: SBML Type "Delay"

Describable-class: Describing objects

Dimensions-class: SBML type "Dimensions"

EventAssignment-class: SBML type "EventAssignment"

Event-class: SBML type "Event"

Experiment-class: Experiment

FunctionDefinition-class: SBML type "FunctionDefinition"

GraphicalObject-class: SBML type "GraphicalObject"

InitialAssignment-class: SBML Type "InitialAssignment"

KineticLaw-class: SBML type "KineticLaw"

Layout-class: SBML type "Layout"

LineSegment-class: SBML type "LineSegment"

math: MathML Utilities

Model-class: SBML type "Model"

ModelCreator-class: SBML Type "ModelCreator"

ModelHistory-class: SBML Type "ModelHistory"

ModifierSpeciesReference-class: SBML type "ModifierSpeciesReference"

Parameter-class: SBML type "Parameter"

ParameterRule-class: SBML type "ParameterRule"

Point-class: SBML type "Point"

RateRule-class: SBML type "RateRule"

Reaction-class: SBML type "Reaction"

ReactionGlyph-class: SBML type "ReactionGlyph"

read: Read in an SBML file (start here)

Rule-class: SBML type "Rule"

SBase-class: SBML type "SBase"

SBML-class: SBML type "SBML"

SBMLDocument-class: "SBMLDocument" from libsbml

SBMLProblem-class: SBMLProblem

SBMLProblems-class: SBMLProblems

SimpleSpeciesReference-class: SBML type "SimpleSpeciesReference"

SOSDesign-class: SOSDesign

SOSExperiment-class: SOS Experiment

SOSProtocol-class: SOSProtocol

SOSResult-class: SOSResult

SOSSubject-class: SOSSubject

Species-class: SBML type "Species"

SpeciesConcentrationRule-class: SBML type "SpeciesConcentrationRule"

SpeciesGlyph-class: SBML type "SpeciesGlyph"

SpeciesReference-class: SBML type "SpeciesReference"

SpeciesReferenceGlyph-class: SBML type "SpeciesReferenceGlyph"

SpeciesType-class: SBML Type "SpeciesType"

StoichiometryMath-class: SBML type "StoichiometryMath"

TextGlyph-class: SBML type "TextGlyph"

Trigger-class: SBML Type "Trigger"

Unit-class: SBML type "Unit"

UnitDefinition-class: SBML type "UnitDefinition"

Functions

acot Man page
acoth Man page
acsc Man page
acsch Man page
additionalGraphicalObjects Man page
additionalGraphicalObjects<- Man page
additionalGraphicalObjects<-,Layout-method Man page
additionalGraphicalObjects,Layout-method Man page
AlgebraicRule-class Man page
annotation Man page
annotation<- Man page
annotation<-,SBase-method Man page
annotation,SBase-method Man page
as.character.SBML Man page
as.character.SBMLDocument Man page
asec Man page
asech Man page
AssignmentRule-class Man page
as.ts,SOSResult-method Man page
basePoint1 Man page
basePoint1<- Man page
basePoint1<-,CubicBezier-method Man page
basePoint1,CubicBezier-method Man page
basePoint2 Man page
basePoint2<- Man page
basePoint2<-,CubicBezier-method Man page
basePoint2,CubicBezier-method Man page
biologicalQualifierType Man page
biologicalQualifierType<- Man page
biologicalQualifierType<-,CVTerm-method Man page
biologicalQualifierType,CVTerm-method Man page
boundaryCondition Man page
boundaryCondition<- Man page
boundaryCondition<-,Species-method Man page
boundaryCondition,Species-method Man page
boundingBox Man page
boundingBox<- Man page
BoundingBox-class Man page
boundingBox<-,GraphicalObject-method Man page
boundingBox,GraphicalObject-method Man page
charge Man page
charge<- Man page
charge<-,Species-method Man page
charge,Species-method Man page
coerce Man page
coerce,SBMLDocument,graph-method Man page
coerce,SBMLDocument,SBML-method Man page
coerce,SBML,graph-method Man page
coerce,SBML,SBMLDocument-method Man page
compartment Man page
compartment<- Man page
Compartment-class Man page
compartment<-,CompartmentGlyph-method Man page
compartment,CompartmentGlyph-method Man page
compartment<-,CompartmentVolumeRule-method Man page
compartment,CompartmentVolumeRule-method Man page
CompartmentGlyph-class Man page
compartmentGlyphs Man page
compartmentGlyphs<- Man page
compartmentGlyphs<-,Layout-method Man page
compartmentGlyphs,Layout-method Man page
compartments Man page
compartments<- Man page
compartments<-,Model-method Man page
compartments,Model-method Man page
compartment<-,Species-method Man page
compartment,Species-method Man page
compartments,SOSResult-method Man page
CompartmentType-class Man page
compartmentTypes Man page
compartmentTypes<- Man page
compartmentTypes<-,Model-method Man page
compartmentTypes,Model-method Man page
CompartmentVolumeRule-class Man page
.condition,SBMLProblem-method Man page
constant Man page
constant<- Man page
constant<-,Compartment-method Man page
constant,Compartment-method Man page
constant<-,Parameter-method Man page
constant,Parameter-method Man page
constant<-,Species-method Man page
constant,Species-method Man page
Constraint-class Man page
constraints Man page
constraints<- Man page
constraints<-,Model-method Man page
constraints,Model-method Man page
cot Man page
coth Man page
createdDate Man page
createdDate<- Man page
createdDate<-,ModelHistory,character-method Man page
createdDate,ModelHistory-method Man page
createdDate,ModelHistory-method Man page
createdDate<-,ModelHistory,POSIXt-method Man page
creators Man page
creators<- Man page
creators<-,ModelHistory-method Man page
creators,ModelHistory-method Man page
csc Man page
csch Man page
CubicBezier-class Man page
Curve-class Man page
curveSegments Man page
curveSegments<- Man page
curveSegments<-,Curve-method Man page
curveSegments,Curve-method Man page
CVTerm-class Man page
cvTerms Man page
cvTerms<- Man page
cvTerms<-,SBase-method Man page
cvTerms,SBase-method Man page
Delay-class Man page
depth Man page
depth<- Man page
depth<-,Dimensions-method Man page
depth,Dimensions-method Man page
Describable-class Man page
describe Man page
describe,AlgebraicRule-method Man page
describe,AssignmentRule-method Man page
describe,BoundingBox-method Man page
describe,CompartmentGlyph-method Man page
describe,Compartment-method Man page
describe,CompartmentType-method Man page
describe,CompartmentVolumeRule-method Man page
describe,Constraint-method Man page
describe,CubicBezier-method Man page
describe,Curve-method Man page
describe,CVTerm-method Man page
describe,Delay-method Man page
describe,Dimensions-method Man page
describe,EventAssignment-method Man page
describe,Event-method Man page
describe,FunctionDefinition-method Man page
describe,GraphicalObject-method Man page
describe,InitialAssignment-method Man page
describe,KineticLaw-method Man page
describe,Layout-method Man page
describe,LineSegment-method Man page
describe,list-method Man page
describe-methods Man page
describe,ModelCreator-method Man page
describe,ModelHistory-method Man page
describe,Model-method Man page
describe,Parameter-method Man page
describe,ParameterRule-method Man page
describe,Point-method Man page
describe,RateRule-method Man page
describe,ReactionGlyph-method Man page
describe,Reaction-method Man page
describe,SBML-method Man page
describe,SimpleSpeciesReference-method Man page
describe,SpeciesConcentrationRule-method Man page
describe,SpeciesGlyph-method Man page
describe,Species-method Man page
describe,SpeciesReferenceGlyph-method Man page
describe,SpeciesReference-method Man page
describe,SpeciesType-method Man page
describe,StoichiometryMath-method Man page
describe,TextGlyph-method Man page
describe,Trigger-method Man page
describe,UnitDefinition-method Man page
describe,Unit-method Man page
design Man page
design<- Man page
design<-,Experiment-method Man page
design,Experiment-method Man page
dimensions Man page
dimensions<- Man page
dimensions<-,BoundingBox-method Man page
dimensions,BoundingBox-method Man page
Dimensions-class Man page
dimensions<-,Layout-method Man page
dimensions,Layout-method Man page
email Man page
email<- Man page
email<-,ModelCreator-method Man page
email,ModelCreator-method Man page
end Man page
end<- Man page
end<-,LineSegment-method Man page
end,LineSegment-method Man page
errors Man page
errors,SBMLProblems-method Man page
EventAssignment-class Man page
eventAssignments Man page
eventAssignments<- Man page
eventAssignments<-,Event-method Man page
eventAssignments,Event-method Man page
Event-class Man page
eventDelay Man page
eventDelay<- Man page
eventDelay<-,Event-method Man page
eventDelay,Event-method Man page
events Man page
events<- Man page
events<-,Model-method Man page
events,Model-method Man page
Experiment-class Man page
ExperimentDesign-class Man page
ExperimentProtocol-class Man page
ExperimentResult-class Man page
ExperimentSubject-class Man page
exponent Man page
exponent<- Man page
exponent<-,Unit-method Man page
exponent,Unit-method Man page
familyName Man page
familyName<- Man page
familyName<-,ModelCreator-method Man page
familyName,ModelCreator-method Man page
fast Man page
fast<- Man page
fast<-,Reaction-method Man page
fast,Reaction-method Man page
fatals Man page
fatals,SBMLProblems-method Man page
FunctionDefinition-class Man page
functionDefinitions Man page
functionDefinitions<- Man page
functionDefinitions<-,Model-method Man page
functionDefinitions,Model-method Man page
givenName Man page
givenName<- Man page
givenName<-,ModelCreator-method Man page
givenName,ModelCreator-method Man page
glyphCurve Man page
glyphCurve<- Man page
glyphCurve<-,ReactionGlyph-method Man page
glyphCurve,ReactionGlyph-method Man page
glyphCurve<-,SpeciesReferenceGlyph-method Man page
glyphCurve,SpeciesReferenceGlyph-method Man page
graphicalObject Man page
graphicalObject<- Man page
GraphicalObject-class Man page
graphicalObject<-,TextGlyph-method Man page
graphicalObject,TextGlyph-method Man page
hasOnlySubstanceUnits Man page
hasOnlySubstanceUnits<- Man page
hasOnlySubstanceUnits<-,Species-method Man page
hasOnlySubstanceUnits,Species-method Man page
height Man page
height<- Man page
height<-,Dimensions-method Man page
height,Dimensions-method Man page
id Man page
id<- Man page
id<-,BoundingBox-method Man page
id,BoundingBox-method Man page
id<-,Compartment-method Man page
id,Compartment-method Man page
id<-,CompartmentType-method Man page
id,CompartmentType-method Man page
id<-,Event-method Man page
id,Event-method Man page
id<-,FunctionDefinition-method Man page
id,FunctionDefinition-method Man page
id<-,GraphicalObject-method Man page
id,GraphicalObject-method Man page
id<-,Layout-method Man page
id,Layout-method Man page
id<-,Model-method Man page
id,Model-method Man page
id<-,Parameter-method Man page
id,Parameter-method Man page
id<-,Reaction-method Man page
id,Reaction-method Man page
id<-,SimpleSpeciesReference-method Man page
id,SimpleSpeciesReference-method Man page
id<-,Species-method Man page
id,Species-method Man page
id<-,SpeciesType-method Man page
id,SpeciesType-method Man page
id<-,UnitDefinition-method Man page
id,UnitDefinition-method Man page
infos Man page
infos,SBMLProblems-method Man page
initialAmount Man page
initialAmount<- Man page
initialAmount<-,Species-method Man page
initialAmount,Species-method Man page
InitialAssignment-class Man page
initialAssignments Man page
initialAssignments<- Man page
initialAssignments<-,Model-method Man page
initialAssignments,Model-method Man page
initialConcentration Man page
initialConcentration<- Man page
initialConcentration<-,Species-method Man page
initialConcentration,Species-method Man page
kind Man page
kind<- Man page
kind<-,Unit-method Man page
kind,Unit-method Man page
kineticLaw Man page
kineticLaw<- Man page
KineticLaw-class Man page
kineticLaw<-,Reaction-method Man page
kineticLaw,Reaction-method Man page
Layout-class Man page
layouts Man page
layouts<- Man page
layouts<-,Model-method Man page
layouts,Model-method Man page
level Man page
level<- Man page
level<-,SBML-method Man page
level,SBML-method Man page
LineSegment-class Man page
math Man page
math<- Man page
math<-,Constraint-method Man page
math,Constraint-method Man page
math<-,Delay-method Man page
math,Delay-method Man page
math<-,EventAssignment-method Man page
math,EventAssignment-method Man page
math<-,FunctionDefinition-method Man page
math,FunctionDefinition-method Man page
math<-,InitialAssignment-method Man page
math,InitialAssignment-method Man page
math<-,KineticLaw-method Man page
math,KineticLaw-method Man page
math<-,ParameterRule-method Man page
math,ParameterRule-method Man page
math<-,Rule-method Man page
math,Rule-method Man page
math<-,StoichiometryMath-method Man page
math,StoichiometryMath-method Man page
math<-,Trigger-method Man page
math,Trigger-method Man page
metaId Man page
metaId<- Man page
metaId<-,SBase-method Man page
metaId,SBase-method Man page
model Man page
model<- Man page
Model-class Man page
ModelCreator-class Man page
modelHistory Man page
modelHistory<- Man page
ModelHistory-class Man page
modelHistory<-,Model-method Man page
modelHistory,Model-method Man page
modelQualifierType Man page
modelQualifierType<- Man page
modelQualifierType<-,CVTerm-method Man page
modelQualifierType,CVTerm-method Man page
model<-,SBML-method Man page
model,SBML-method Man page
modifiedDate Man page
modifiedDate<- Man page
modifiedDate<-,ModelHistory,character-method Man page
modifiedDate<-,ModelHistory-method Man page
modifiedDate,ModelHistory-method Man page
modifiedDate<-,ModelHistory,POSIXt-method Man page
modifiers Man page
modifiers<- Man page
ModifierSpeciesReference-class Man page
modifiers<-,Reaction-method Man page
modifiers,Reaction-method Man page
msg Man page
msg<- Man page
msg<-,Constraint-method Man page
msg,Constraint-method Man page
multiplier Man page
multiplier<- Man page
multiplier<-,Unit-method Man page
multiplier,Unit-method Man page
name Man page
name<- Man page
name<-,Compartment-method Man page
name,Compartment-method Man page
name<-,CompartmentType-method Man page
name,CompartmentType-method Man page
name<-,Event-method Man page
name,Event-method Man page
name<-,FunctionDefinition-method Man page
name,FunctionDefinition-method Man page
name<-,Model-method Man page
name,Model-method Man page
name<-,Parameter-method Man page
name,Parameter-method Man page
name<-,ParameterRule-method Man page
name,ParameterRule-method Man page
name<-,Reaction-method Man page
name,Reaction-method Man page
name<-,Species-method Man page
name,Species-method Man page
name<-,SpeciesType-method Man page
name,SpeciesType-method Man page
name<-,UnitDefinition-method Man page
name,UnitDefinition-method Man page
notes Man page
notes<- Man page
notes<-,SBase-method Man page
notes,SBase-method Man page
offset Man page
offset<- Man page
offset<-,Unit-method Man page
offset,Unit-method Man page
OptionalCurve-class Man page
OptionalDelay-class Man page
OptionalKineticLaw-class Man page
OptionalModelHistory-class Man page
OptionalStoichiometryMath-class Man page
organization Man page
organization<- Man page
organization<-,ModelCreator-method Man page
organization,ModelCreator-method Man page
originOfText Man page
originOfText<- Man page
originOfText<-,TextGlyph-method Man page
originOfText,TextGlyph-method Man page
outside Man page
outside<- Man page
outside<-,Compartment-method Man page
outside,Compartment-method Man page
Parameter-class Man page
ParameterRule-class Man page
parameters Man page
parameters<- Man page
parameters<-,KineticLaw-method Man page
parameters,KineticLaw-method Man page
parameters<-,Model-method Man page
parameters,Model-method Man page
parameters,SOSResult-method Man page
Point-class Man page
position Man page
position<- Man page
position<-,BoundingBox-method Man page
position,BoundingBox-method Man page
products Man page
products<- Man page
products<-,Reaction-method Man page
products,Reaction-method Man page
protocol Man page
protocol<- Man page
protocol<-,Experiment-method Man page
protocol,Experiment-method Man page
qualifierType Man page
qualifierType<- Man page
qualifierType<-,CVTerm-method Man page
qualifierType,CVTerm-method Man page
RateRule-class Man page
reactants Man page
reactants<- Man page
reactants<-,Reaction-method Man page
reactants,Reaction-method Man page
reaction Man page
reaction<- Man page
Reaction-class Man page
ReactionGlyph-class Man page
reactionGlyphs Man page
reactionGlyphs<- Man page
reactionGlyphs<-,Layout-method Man page
reactionGlyphs,Layout-method Man page
reaction<-,ReactionGlyph-method Man page
reaction,ReactionGlyph-method Man page
reactions Man page
reactions<- Man page
reactions<-,Experiment-method Man page
reactions<-,Model-method Man page
reactions,Model-method Man page
reactions<-,SOSDesign-method Man page
reactions,SOSDesign-method Man page
reactions,SOSResult-method Man page
resources Man page
resources<- Man page
resources<-,CVTerm-method Man page
resources,CVTerm-method Man page
result Man page
result<- Man page
result<-,Experiment-method Man page
result,Experiment-method Man page
reversible Man page
reversible<- Man page
reversible<-,Reaction-method Man page
reversible,Reaction-method Man page
role Man page
role<- Man page
role<-,SpeciesReferenceGlyph-method Man page
role,SpeciesReferenceGlyph-method Man page
rsbml_check Man page
rsbml_check,SBMLDocument-method Man page
rsbml_check,SBML-method Man page
rsbml_doc Man page
rsbml_doc,SBML-method Man page
rsbml_dom Man page
rsbml_dom,SBMLDocument-method Man page
rsbml_graph Man page
rsbml_graph,Model-method Man page
rsbml_graph,SBMLDocument-method Man page
rsbml_graph,SBML-method Man page
rsbml_problems Man page
rsbml_problems,SBMLDocument-method Man page
rsbml_read Man page
rsbml_write Man page
rsbml_write,SBMLDocument-method Man page
rsbml_write,SBML-method Man page
rsbml_xml Man page
rsbml_xml,SBMLDocument-method Man page
rsbml_xml,SBML-method Man page
Rule-class Man page
rules Man page
rules<- Man page
rules<-,Model-method Man page
rules,Model-method Man page
SBase-class Man page
SBML-class Man page
SBMLDocument-class Man page
SBMLError-class Man page
SBMLFatal-class Man page
SBMLInfo-class Man page
SBMLProblem-class Man page
SBMLProblems-class Man page
SBMLWarning-class Man page
sboTerm Man page
sboTerm<- Man page
sboTerm<-,SBase-method Man page
sboTerm,SBase-method Man page
sec Man page
sech Man page
show,Describable-method Man page
show,SBMLProblem-method Man page
SimpleSpeciesReference-class Man page
simulate Man page
simulate,SBMLDocument-method Man page
simulate,SBML-method Man page
simulate,SOSExperiment-method Man page
size Man page
size<- Man page
size<-,Compartment-method Man page
size,Compartment-method Man page
SOSDesign-class Man page
SOSExperiment-class Man page
SOSProtocol-class Man page
SOSResult-class Man page
SOSSubject-class Man page
spatialDimensions Man page
spatialDimensions<- Man page
spatialDimensions<-,Compartment-method Man page
spatialDimensions,Compartment-method Man page
spatialSizeUnits Man page
spatialSizeUnits<- Man page
spatialSizeUnits<-,Species-method Man page
spatialSizeUnits,Species-method Man page
species Man page
species<- Man page
Species-class Man page
SpeciesConcentrationRule-class Man page
speciesGlyph Man page
speciesGlyph<- Man page
SpeciesGlyph-class Man page
speciesGlyphs Man page
speciesGlyphs<- Man page
speciesGlyphs<-,Layout-method Man page
speciesGlyphs,Layout-method Man page
speciesGlyph<-,SpeciesReferenceGlyph-method Man page
speciesGlyph,SpeciesReferenceGlyph-method Man page
species<-,Model-method Man page
species,Model-method Man page
speciesReference Man page
speciesReference<- Man page
SpeciesReference-class Man page
SpeciesReferenceGlyph-class Man page
speciesReferenceGlyphs Man page
speciesReferenceGlyphs<- Man page
speciesReferenceGlyphs<-,ReactionGlyph-method Man page
speciesReferenceGlyphs,ReactionGlyph-method Man page
speciesReference<-,SpeciesReferenceGlyph-method Man page
speciesReference,SpeciesReferenceGlyph-method Man page
species<-,SimpleSpeciesReference-method Man page
species,SimpleSpeciesReference-method Man page
species,SOSResult-method Man page
species<-,SpeciesConcentrationRule-method Man page
species,SpeciesConcentrationRule-method Man page
species<-,SpeciesGlyph-method Man page
species,SpeciesGlyph-method Man page
SpeciesType-class Man page
speciesTypes Man page
speciesTypes<- Man page
speciesTypes<-,Model-method Man page
speciesTypes,Model-method Man page
start Man page
start<- Man page
start<-,LineSegment-method Man page
start,LineSegment-method Man page
stoichiometry Man page
stoichiometry<- Man page
stoichiometryMath Man page
stoichiometryMath<- Man page
StoichiometryMath-class Man page
stoichiometryMath<-,SpeciesReference-method Man page
stoichiometryMath,SpeciesReference-method Man page
stoichiometryMatrix Man page
stoichiometryMatrix,Model-method Man page
stoichiometry<-,SpeciesReference-method Man page
stoichiometry,SpeciesReference-method Man page
subject Man page
subject<- Man page
subject<-,Experiment-method Man page
subject,Experiment-method Man page
substanceUnits Man page
substanceUnits<- Man page
substanceUnits<-,KineticLaw-method Man page
substanceUnits,KineticLaw-method Man page
substanceUnits<-,Species-method Man page
substanceUnits,Species-method Man page
symbol Man page
symbol<- Man page
symbol<-,InitialAssignment-method Man page
symbol,InitialAssignment-method Man page
text Man page
text<- Man page
TextGlyph-class Man page
textGlyphs Man page
textGlyphs<- Man page
textGlyphs<-,Layout-method Man page
textGlyphs,Layout-method Man page
text<-,TextGlyph-method Man page
text,TextGlyph-method Man page
.throw,SBMLError-method Man page
.throw,SBMLFatal-method Man page
.throw,SBMLInfo-method Man page
.throw,SBMLProblems-method Man page
.throw,SBMLWarning-method Man page
timeUnits Man page
timeUnits<- Man page
timeUnits<-,Event-method Man page
timeUnits,Event-method Man page
timeUnits<-,KineticLaw-method Man page
timeUnits,KineticLaw-method Man page
trigger Man page
trigger<- Man page
Trigger-class Man page
trigger<-,Event-method Man page
trigger,Event-method Man page
type Man page
type<- Man page
type<-,AssignmentRule-method Man page
type,AssignmentRule-method Man page
type<-,ParameterRule-method Man page
type,ParameterRule-method Man page
Unit-class Man page
UnitDefinition-class Man page
unitDefinitions Man page
unitDefinitions<- Man page
unitDefinitions<-,Model-method Man page
unitDefinitions,Model-method Man page
units Man page
units<- Man page
unitScale Man page
unitScale<- Man page
unitScale<-,Unit-method Man page
unitScale,Unit-method Man page
units<-,Compartment-method Man page
units,Compartment-method Man page
units<-,Parameter-method Man page
units,Parameter-method Man page
units<-,ParameterRule-method Man page
units,ParameterRule-method Man page
units<-,Species-method Man page
units,Species-method Man page
units<-,UnitDefinition-method Man page
units,UnitDefinition-method Man page
value Man page
value<- Man page
value<-,Parameter-method Man page
value,Parameter-method Man page
variable Man page
variable<- Man page
variable<-,AssignmentRule-method Man page
variable,AssignmentRule-method Man page
variable<-,EventAssignment-method Man page
variable,EventAssignment-method Man page
variable<-,ParameterRule-method Man page
variable,ParameterRule-method Man page
variable<-,RateRule-method Man page
variable,RateRule-method Man page
ver Man page
ver<- Man page
ver<-,SBML-method Man page
ver,SBML-method Man page
warns Man page
warns,SBMLProblems-method Man page
width Man page
width<- Man page
width<-,Dimensions-method Man page
width,Dimensions-method Man page
x Man page
x<- Man page
x<-,Point-method Man page
x,Point-method Man page
y Man page
y<- Man page
y<-,Point-method Man page
y,Point-method Man page
z Man page
z<- Man page
z<-,Point-method Man page
z,Point-method Man page

Files

rsbml/DESCRIPTION
rsbml/INSTALL
rsbml/NAMESPACE
rsbml/NEWS
rsbml/R
rsbml/R/AAADescribable.R rsbml/R/AAASBase.R rsbml/R/AADimensions.R rsbml/R/AAPoint.R rsbml/R/AARule.R rsbml/R/AAStoichiometryMath.R rsbml/R/ABoundingBox.R rsbml/R/ACompartmentType.R rsbml/R/ACurve.R rsbml/R/AEventAssignment.R rsbml/R/AGraphicalObject.R rsbml/R/ALineSegment.R rsbml/R/AModelCreator.R rsbml/R/AModelHistory.R rsbml/R/ASimpleSpeciesReference.R rsbml/R/ASpeciesReference.R rsbml/R/ASpeciesReferenceGlyph.R rsbml/R/ASpeciesType.R rsbml/R/ATrigger.R rsbml/R/AlgebraicRule.R rsbml/R/AssignmentRule.R rsbml/R/CVTerm.R rsbml/R/Compartment.R rsbml/R/CompartmentGlyph.R rsbml/R/CompartmentVolumeRule.R rsbml/R/Constraint.R rsbml/R/CubicBezier.R rsbml/R/Delay.R rsbml/R/Event.R rsbml/R/FunctionDefinition.R rsbml/R/InitialAssignment.R rsbml/R/KineticLaw.R rsbml/R/Layout.R rsbml/R/Model.R rsbml/R/ModifierSpeciesReference.R rsbml/R/Parameter.R rsbml/R/ParameterRule.R rsbml/R/RateRule.R rsbml/R/Reaction.R rsbml/R/ReactionGlyph.R rsbml/R/SBML.R rsbml/R/Species.R rsbml/R/SpeciesConcentrationRule.R rsbml/R/SpeciesGlyph.R rsbml/R/TextGlyph.R rsbml/R/Unit.R rsbml/R/UnitDefinition.R rsbml/R/aaa.R rsbml/R/graph.R rsbml/R/math.R rsbml/R/problems.R rsbml/R/rsbml.R rsbml/R/simulate.R rsbml/R/utils.R rsbml/R/zzz.R
rsbml/build
rsbml/build/vignette.rds
rsbml/configure
rsbml/configure.in
rsbml/inst
rsbml/inst/SBML_odeSolver-1.7.0beta
rsbml/inst/SBML_odeSolver-1.7.0beta/AUTHORS
rsbml/inst/SBML_odeSolver-1.7.0beta/COPYING
rsbml/inst/SBML_odeSolver-1.7.0beta/ChangeLog
rsbml/inst/SBML_odeSolver-1.7.0beta/INSTALL
rsbml/inst/SBML_odeSolver-1.7.0beta/Makefile.am
rsbml/inst/SBML_odeSolver-1.7.0beta/Makefile.in
rsbml/inst/SBML_odeSolver-1.7.0beta/NEWS
rsbml/inst/SBML_odeSolver-1.7.0beta/OUTLOOK
rsbml/inst/SBML_odeSolver-1.7.0beta/README
rsbml/inst/SBML_odeSolver-1.7.0beta/SOSlib.doxy
rsbml/inst/SBML_odeSolver-1.7.0beta/TODO
rsbml/inst/SBML_odeSolver-1.7.0beta/VERSION.txt
rsbml/inst/SBML_odeSolver-1.7.0beta/aclocal.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config
rsbml/inst/SBML_odeSolver-1.7.0beta/config.log
rsbml/inst/SBML_odeSolver-1.7.0beta/config/ax_compare_version.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/config.guess
rsbml/inst/SBML_odeSolver-1.7.0beta/config/config.sub
rsbml/inst/SBML_odeSolver-1.7.0beta/config/cvode.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/depcomp
rsbml/inst/SBML_odeSolver-1.7.0beta/config/fpic.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/grace.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/graphviz.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/install-sh
rsbml/inst/SBML_odeSolver-1.7.0beta/config/missing
rsbml/inst/SBML_odeSolver-1.7.0beta/config/sbml.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/sundials.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/config/tcc.m4
rsbml/inst/SBML_odeSolver-1.7.0beta/configure
rsbml/inst/SBML_odeSolver-1.7.0beta/configure.in
rsbml/inst/SBML_odeSolver-1.7.0beta/configure.lineno
rsbml/inst/SBML_odeSolver-1.7.0beta/doc
rsbml/inst/SBML_odeSolver-1.7.0beta/doc/README
rsbml/inst/SBML_odeSolver-1.7.0beta/odeSolver.doxy
rsbml/inst/SBML_odeSolver-1.7.0beta/scripts
rsbml/inst/SBML_odeSolver-1.7.0beta/scripts/gnuplotscript.awk
rsbml/inst/SBML_odeSolver-1.7.0beta/scripts/xmgracefile.pl
rsbml/inst/SBML_odeSolver-1.7.0beta/src
rsbml/inst/SBML_odeSolver-1.7.0beta/src/ASTIndexNameNode.cpp
rsbml/inst/SBML_odeSolver-1.7.0beta/src/Makefile.am
rsbml/inst/SBML_odeSolver-1.7.0beta/src/Makefile.in
rsbml/inst/SBML_odeSolver-1.7.0beta/src/arithmeticCompiler.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/charBuffer.cpp
rsbml/inst/SBML_odeSolver-1.7.0beta/src/compiler.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/cvodeData.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/cvodeSolver.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/daeSolver.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/drawGraph.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/integratorInstance.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/integratorSettings.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/interpol.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/libODES.pc
rsbml/inst/SBML_odeSolver-1.7.0beta/src/libODES.pc.in
rsbml/inst/SBML_odeSolver-1.7.0beta/src/modelSimplify.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/nullSolver.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/odeConstruct.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/odeModel.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/odeSolver.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/processAST.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbml.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlResults.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/Makefile
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/arithmeticCompiler.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/arithmeticCompilerTest.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTCompiler/interfaceSimulation.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/ASTIndexNameNode.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/arithmeticCompiler.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/charBuffer.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/compiler.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/config.h.in
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/cvodeData.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/cvodeSolver.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/daeSolver.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/drawGraph.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/exportdefs.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/integratorInstance.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/integratorSettings.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/interpol.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/modelSimplify.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/nullSolver.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/odeConstruct.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/odeModel.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/odeSolver.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/processAST.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/sbml.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/sbmlResults.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/sensSolver.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/solverError.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/stamp-h1
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/util.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sbmlsolver/variableIndex.h
rsbml/inst/SBML_odeSolver-1.7.0beta/src/sensSolver.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/solverError.c
rsbml/inst/SBML_odeSolver-1.7.0beta/src/util.c
rsbml/inst/doc
rsbml/inst/doc/quick-start.R
rsbml/inst/doc/quick-start.Rnw
rsbml/inst/doc/quick-start.pdf
rsbml/inst/gen
rsbml/inst/gen/gen.R
rsbml/inst/sbml
rsbml/inst/sbml/GlycolysisLayout.xml
rsbml/inst/sbml/biotin-fa.xml
rsbml/inst/sbml/cell-cycle.xml
rsbml/inst/sbml/curto.xml
rsbml/inst/sbml/squid-axon.xml
rsbml/inst/tests
rsbml/inst/tests/l1v1-branch-schema-error.xml
rsbml/inst/tests/l1v1-branch.xml
rsbml/inst/tests/l1v1-minimal.xml
rsbml/inst/tests/l1v1-rules.xml
rsbml/inst/tests/l1v1-units.xml
rsbml/inst/tests/l1v2-branch.xml
rsbml/inst/tests/l2v1-2D-compartments.xml
rsbml/inst/tests/l2v1-algebraic.xml
rsbml/inst/tests/l2v1-assignment.xml
rsbml/inst/tests/l2v1-boundary.xml
rsbml/inst/tests/l2v1-branch.xml
rsbml/inst/tests/l2v1-delay.xml
rsbml/inst/tests/l2v1-events.xml
rsbml/inst/tests/l2v1-functions.xml
rsbml/inst/tests/l2v1-mc-ode.xml
rsbml/inst/tests/l2v1-units.xml
rsbml/man
rsbml/man/AlgebraicRule-class.Rd rsbml/man/AssignmentRule-class.Rd rsbml/man/BoundingBox-class.Rd rsbml/man/CVTerm-class.Rd rsbml/man/Compartment-class.Rd rsbml/man/CompartmentGlyph-class.Rd rsbml/man/CompartmentType-class.Rd rsbml/man/CompartmentVolumeRule-class.Rd rsbml/man/Constraint-class.Rd rsbml/man/CubicBezier-class.Rd rsbml/man/Curve-class.Rd rsbml/man/Delay-class.Rd rsbml/man/Describable-class.Rd rsbml/man/Dimensions-class.Rd rsbml/man/Event-class.Rd rsbml/man/EventAssignment-class.Rd rsbml/man/Experiment-class.Rd rsbml/man/FunctionDefinition-class.Rd rsbml/man/GraphicalObject-class.Rd rsbml/man/InitialAssignment-class.Rd rsbml/man/KineticLaw-class.Rd rsbml/man/Layout-class.Rd rsbml/man/LineSegment-class.Rd rsbml/man/Model-class.Rd rsbml/man/ModelCreator-class.Rd rsbml/man/ModelHistory-class.Rd rsbml/man/ModifierSpeciesReference-class.Rd rsbml/man/Parameter-class.Rd rsbml/man/ParameterRule-class.Rd rsbml/man/Point-class.Rd rsbml/man/RateRule-class.Rd rsbml/man/Reaction-class.Rd rsbml/man/ReactionGlyph-class.Rd rsbml/man/Rule-class.Rd rsbml/man/SBML-class.Rd rsbml/man/SBMLDocument-class.Rd rsbml/man/SBMLProblem-class.Rd rsbml/man/SBMLProblems-class.Rd rsbml/man/SBase-class.Rd rsbml/man/SOSDesign-class.Rd rsbml/man/SOSExperiment-class.Rd rsbml/man/SOSProtocol-class.Rd rsbml/man/SOSResult-class.Rd rsbml/man/SOSSubject-class.Rd rsbml/man/SimpleSpeciesReference-class.Rd rsbml/man/Species-class.Rd rsbml/man/SpeciesConcentrationRule-class.Rd rsbml/man/SpeciesGlyph-class.Rd rsbml/man/SpeciesReference-class.Rd rsbml/man/SpeciesReferenceGlyph-class.Rd rsbml/man/SpeciesType-class.Rd rsbml/man/StoichiometryMath-class.Rd rsbml/man/TextGlyph-class.Rd rsbml/man/Trigger-class.Rd rsbml/man/Unit-class.Rd rsbml/man/UnitDefinition-class.Rd rsbml/man/math.Rd rsbml/man/read.Rd
rsbml/src
rsbml/src/Makevars
rsbml/src/Makevars.in
rsbml/src/Makevars.win
rsbml/src/StringMap.c
rsbml/src/StringMap.h
rsbml/src/check.c
rsbml/src/doc.c
rsbml/src/dom.c
rsbml/src/graph.c
rsbml/src/init.c
rsbml/src/io.c
rsbml/src/layoutWrappers.cpp
rsbml/src/mathml.c
rsbml/src/rsbml.h
rsbml/src/simulate.c
rsbml/start.R
rsbml/vignettes
rsbml/vignettes/quick-start.Rnw
rsbml/vignettes/rsbml.bib

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