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"

Files in this package

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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