| Title: | R support for SBML, using libsbml |
|---|---|
| Description: | 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. |
| Authors: | Michael Lawrence <[email protected]> |
| Maintainer: | Michael Lawrence <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 2.63.0 |
| Built: | 2024-07-03 06:32:09 UTC |
| Source: | https://github.com/bioc/rsbml |
Expresses equations that are not assignments nor rates of change.
Objects can be created by calls of the form new("AlgebraicRule", ...).
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "Rule", directly.
Class "SBase", by class "Rule", distance 2.
No methods defined with class "AlgebraicRule" in the signature.
Michael Lawrence
An equation that assigns a value to the quantity of a
Species, the size of a Compartment
or the value of a Parameter.
Objects can be created by calls of the form new("AssignmentRule", ...).
variable:Object of class "character" naming the
variable (the id of a Species, Compartment
or Parameter) to set.
type:Object of class "character", deprecated.
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "Rule", directly.
Class "SBase", by class "Rule", distance 2.
signature(object = "AssignmentRule"): gets the variable slot
signature(object = "AssignmentRule"): sets the variable slot
signature(object = "AssignmentRule"): gets the type slot
signature(object = "AssignmentRule"): sets the type slot
Michael Lawrence
Species the size and position of an SBML layout object.
Objects can be created by calls of the form new("BoundingBox", ...).
id:Object of class "character" uniquely identifying this component.
position:Object of class "Point" specifying the positon.
dimensions:Object of class "Dimensions" specifying the size.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "BoundingBox"): gets the id slot
signature(object = "BoundingBox"): sets the id slot
signature(object = "BoundingBox"): gets the dimensions slot
signature(object = "BoundingBox"): sets the dimensions slot
signature(object = "BoundingBox"): gets the position slot
signature(object = "BoundingBox"): sets the position slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
A bounded space that contains Species.
Objects can be created by calls of the form new("Compartment", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
spatialDimensions:Object of class "integer" indicating
the number of dimensions (0, 1, 2, or 3)
size:Object of class "numeric" indicating the size in
the given units.
units:Object of class "character" indicating the units
(built-in or the id of a UnitDefinition).
outside:Object of class "character" identifying the
compartment containing this compartment.
constant:Object of class "logical" indicating whether
the size changes during simulation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Compartment"): gets the id slot
signature(object = "Compartment"): sets the id slot
signature(object = "Compartment"): gets the name slot
signature(object = "Compartment"): sets the name slot
signature(object = "Compartment"): gets the constant slot
signature(object = "Compartment"): sets the constant slot
signature(object = "Compartment"): gets the outside slot
signature(object = "Compartment"): sets the outside slot
signature(object = "Compartment"): gets the size slot
signature(object = "Compartment"): sets the size slot
signature(object = "Compartment"): gets the constant slot
signature(object = "Compartment"): sets the constant slot
signature(object = "Compartment"): gets the spatialDimensions slot
signature(object = "Compartment"): sets the spatialDimensions slot
Michael Lawrence
A glyph representing a Compartment.
Objects can be created by calls of the form new("CompartmentGlyph", ...).
compartment:Object of class "character" identifying the
compartment this glyph represents.
id:Object of class "character" uniquely identifying this component.
boundingBox:Object of class "BoundingBox" describing
the position and size of the graphical object.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "GraphicalObject", directly.
Class "SBase", by class "GraphicalObject", distance 2.
signature(object = "CompartmentGlyph"): gets the compartment slot
signature(object = "CompartmentGlyph"): sets the compartment slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Declares a type of Compartment. Compartments
with the same type are logically similar.
Objects can be created by calls of the form new("CompartmentType", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "CompartmentType"): gets the id slot
signature(object = "CompartmentType"): sets the id slot
signature(object = "CompartmentType"): gets the name slot
signature(object = "CompartmentType"): sets the name slot
Requires libsbml >= 3.0
Michael Lawrence
Obsolete way to assign a volume to a Compartment.
Objects can be created by calls of the form new("CompartmentVolumeRule", ...).
compartment:Object of class "character" identifying the compartment
variable:Object of class "character", ignored.
type:Object of class "character", deprecated.
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "AssignmentRule", directly.
Class "Rule", by class "AssignmentRule", distance 2.
Class "SBase", by class "AssignmentRule", distance 3.
signature(object = "CompartmentVolumeRule"): gets the compartment slot
signature(object = "CompartmentVolumeRule"): sets the compartment slot
Michael Lawrence
A constraint that must be continuously satisfied throughout the simulation of a model. Once a constraint is no longer met, the simulation must halt.
Objects can be created by calls of the form new("Constraint", ...).
math:Object of class "expression" that evaluates to FALSE
if the constraint is not satisfied, otherwise evaluates to TRUE.
message:Object of class "character", formatted in XHTML,
that is displayed to the user by an application when the constraint is not satisfied.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(domain = "Constraint"): gets the math slot.
signature(object = "Constraint"): sets the math slot.
signature(domain = "Constraint"): gets the msg slot.
signature(object = "Constraint"): sets the msg slot.
Requires libsbml >= 3.0
Michael Lawrence
A cubic bezier curve in an SBML layout.
Objects can be created by calls of the form new("CubicBezier", ...).
basePoint1:Object of class "Point" indicating the
position of the base point closest to the starting point.
basePoint2:Object of class "Point" indicating the
position of the base point farthest from the starting point.
start:Object of class "Point" ~~
end:Object of class "Point" ~~
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "LineSegment", directly.
Class "SBase", by class "LineSegment", distance 2.
signature(object = "CubicBezier"): gets the basePoint1 slot
signature(object = "CubicBezier"): sets the basePoint1 slot
signature(object = "CubicBezier"): gets the basePoint2 slot
signature(object = "CubicBezier"): sets the basePoint2 slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
A curve (list of line segments) in an SBML layout.
Objects can be created by calls of the form new("Curve", ...).
curveSegments:Object of class "list" containing the
LineSegments that compose the curve.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Curve"): gets the curveSegments slot
signature(object = "Curve"): sets the curveSegments slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
A MIRIAM annotation, consisting of a qualifier ("model", "biological" or something else) and a resource (URI).
Objects can be created by calls of the form new("CVTerm", ...).
qualifierType:Object of class "character"
specifying the type of qualifier for this term. Types "model" and
"biological" have special meaning, but any string may be specified.
modelQualifierType:Object of class "character"
specifying the type of model qualifier, if qualifierType is
set to "model". Types "is" and "isDescribedBy" are formally
defined in MIRIAM, but any string may be specified.
biologicalQualifierType:Object of class
"character" specifying the type of biological qualifier, if
qualifierType is set to "biological". Types "is", "hasPart",
"isPartOf", "isVersionOf", "hasVersion", "isHomologTo",
and "isDescribedBy" are formally defined in MIRIAM, though any
string may be specified.
resources:Object of class "character"
specifying a URI that identifies some resource related an SBML
element by the qualifier.
signature(object = "CVTerm"):
gets the biologicalQualifierType slot.
signature(object =
"CVTerm"):
sets the biologicalQualifierType slot.
signature(object = "CVTerm"):
gets the modelQualifierType slot.
signature(object = "CVTerm"):
sets the modelQualifierType slot.
signature(object = "CVTerm"):
gets the qualifierType slot.
signature(object = "CVTerm"):
sets the qualifierType slot.
signature(object = "CVTerm"):
gets the resources slot.
signature(object = "CVTerm"):
sets the resources slot.
Michael Lawrence
The length of time between the Triggering of an
Event and the execution of its EventAssignments.
Objects can be created by calls of the form new("Delay", ...).
math:Object of class "expression" that evaluates to
a quantity of time.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(domain = "Delay"): gets the math slot.
signature(object = "Delay"): sets the
math slot.
Requires libsbml >= 3.0
Michael Lawrence
Each class in the SBML DOM extends the Describable
class and thus has a describe method, which
describes an object with a short string. This is used by the
show method to output terse textual representations of the DOM.
describe(object, ...)describe(object, ...)
object |
The object to be described. |
... |
Additional arguments for methods. |
A short textual (string) representation of object.
An object that extends
Describable has a method for the describe
generic, and by default Describable objects are shown by
printing the output of describe. Note that Describable
is a virtual tag class, no objects may be
created from it.
signature(object = "Describable"): outputs the
return value of describe.
Michael Lawrence
Holds the size of an SBML layout object.
Objects can be created by calls of the form new("Dimensions", ...).
width:Object of class "numeric" indicating the width, in pixels
height:Object of class "numeric" indicating the height, in pixels
depth:Object of class "numeric" indicating the depth, in pixels
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Dimensions"): gets the depth slot
signature(object = "Dimensions"): sets the depth slot
signature(object = "Dimensions"): gets the height slot
signature(object = "Dimensions"): sets the height slot
signature(object = "Dimensions"): gets the width slot
signature(object = "Dimensions"): sets the width slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Description of a instantaneous, discontinuous change in the model state.
Objects can be created by calls of the form new("Event", ...).
id:Object of class "character" uniquely
identifying this component.
name:Object of class
"character" naming this component.
trigger:Object of class "expression" that
evaluates to TRUE when the event is to be fired.
eventDelay:Object of class "expression" that
evaluates to the time until execution of this event after it has
been fired.
timeUnits:Object of class
"character" identifying the units of the delay.
eventAssignments:Object of class "list"
containing
EventAssignments that are performed at
execution.
useValuesFromTriggerTime:Object of
class "logical". If FALSE, the event is evaluated
after the delay, rather than when the event is executed.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Event"): gets the id slot
signature(object = "Event"): sets the id slot
signature(object = "Event"): gets the name slot
signature(object = "Event"): sets the name slot
signature(object = "Event"): gets the timeUnits slot
signature(object = "Event"): sets the timeUnits slot
signature(x = "Event"): ...
signature(object = "Event"): sets the delay slot
signature(object = "Event"): gets the eventAssignments slot
signature(object = "Event"): sets the eventAssignments slot
signature(object = "Event"): gets the trigger slot
signature(object = "Event"): sets the trigger slot
Michael Lawrence
As part of an event, assigns a value to the quantity of a
Species, the size of a Compartment
or the value of a Parameter.
Objects can be created by calls of the form new("EventAssignment", ...).
variable:Object of class "character" ~~
math:Object of class "expression" that evaluates to
the value to assign.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "EventAssignment"): gets the math slot
signature(object = "EventAssignment"): sets the math slot
signature(object = "EventAssignment"): gets the variable slot
signature(object = "EventAssignment"): sets the variable slot
Michael Lawrence
This class is an abstraction for an experiment, e.g. in a
simulation. An experiment consists of a
ExperimentProtocol, ExperimentDesign,
ExperimentSubject and ExperimentResult.
A virtual Class: No objects may be created from it.
protocol:Object of empty virtual class
ExperimentProtocol, how the experiment was
or is to be performed.
design:Object of empty virtual class
ExperimentDesign, the design of the experiment.
subject:Object of empty virtual class
ExperimentSubject,
the object being observed by the experiment.
result:Object of empty virtual class
ExperimentResult, the result of the experiment.
signature(object = "Experiment"): Gets the
design slot.
signature(object = "Experiment"): Sets the
design slot.
signature(object = "Experiment"): Gets the
protocol slot.
signature(object = "Experiment"): Sets the
protocol slot.
signature(object = "Experiment"): Gets the
result slot.
signature(object = "Experiment"): Sets the
result slot.
signature(object = "Experiment"): Gets the
subject slot.
signature(object = "Experiment"): Sets the
subject slot.
Michael Lawrence
SOSExperiment, an implementation that simulates
SBML modules using the SBML ODE Solver library.
Identifies a mathematical expression so that it may be referenced in other expressions.
Objects can be created by calls of the form new("FunctionDefinition", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
math:Object of class "expression" that defines the function.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "FunctionDefinition"): gets the id slot
signature(object = "FunctionDefinition"): sets the id slot
signature(object = "FunctionDefinition"): gets the name slot
signature(object = "FunctionDefinition"): sets the name slot
signature(object = "FunctionDefinition"): gets the math slot
signature(object = "FunctionDefinition"): sets the math slot
Michael Lawrence
The base class for graphical objects (e.g. glyphs) in SBML layouts.
Objects can be created by calls of the form new("GraphicalObject", ...).
id:Object of class "character" uniquely identifying this component.
boundingBox:Object of class "BoundingBox" describing
the position and size of the graphical object.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "GraphicalObject"): gets the id slot
signature(object = "GraphicalObject"): sets the id slot
signature(object = "GraphicalObject"): gets the boundingBox slot
signature(object = "GraphicalObject"): sets the boundingBox slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Calculates the value of a symbol when the model is initialized.
Objects can be created by calls of the form new("InitialAssignment", ...).
symbol:Object of class "character" to which the
value is assigned.
math:Object of class "expression" that evaluates
to the assigned value.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "InitialAssignment"): gets the math slot.
signature(object = "InitialAssignment"): sets the math slot.
signature(object = "InitialAssignment"): gets the symbol slot.
signature(object = "InitialAssignment"): sets the symbol slot.
Requires libsbml >= 3.0
Michael Lawrence
AssignmentRule, which can set a value at any time but cannot set constants.
Describes the rate of a Reaction.
Objects can be created by calls of the form new("KineticLaw", ...).
math:Object of class "expression" defining the
rate of the reaction.
parameters:Object of class "list" containing
Parameters that may be used
in math. The names of the list correspond to the IDs of the
elements.
timeUnits:Object of class "character" indicating the
units for time.
substanceUnits:Object of class "character" indicating
the units for substance.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "KineticLaw"): gets the math slot
signature(object = "KineticLaw"): sets the math slot
signature(object = "KineticLaw"): gets the substanceUnits slot
signature(object = "KineticLaw"): sets the substanceUnits slot
signature(object = "KineticLaw"): gets the timeUnits slot
signature(object = "KineticLaw"): sets the timeUnits slot
signature(object = "KineticLaw"): gets the parameters slot
signature(object = "KineticLaw"): sets the parameters slot
Michael Lawrence
Contains the glyphs and other graphical objects that compose an SBML layout. Layouts are not part of the core SBML specification. See the reference for the SBML layout extension specification.
Objects can be created by calls of the form new("Layout", ...).
id:Object of class "character" uniquely
identifying this component.
dimensions:Object of
class "Dimensions" specifing the size of the layout.
compartmentGlyphs:Object of class "list"
containing the CompartmentGlyphs. The names of
the list correspond to the IDs of the elements.
speciesGlyphs:Object of class "list"
containing the SpeciesGlyphs. The names of the
list correspond to the IDs of the elements.
reactionGlyphs:Object of class "list"
containing the ReactionGlyphs. The names of the
list correspond to the IDs of the
elements.
textGlyphs:Object of class "list"
containing the TextGlyphs. The names of the
list correspond to the IDs of the
elements.
additionalGraphicalObjects:Object of
class "list" containing the
additional GraphicalObjects that are not bound
to any model component. The names of the list correspond to the IDs
of the elements.
metaId:Object of
class "character" that is an XML ID "described" by an RDF
resource. This links an SBML element to an RDF resource. RDF may
appear anywhere in an SBML element, but is usually placed inside
the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Layout"): gets the id slot
signature(object = "Layout"): sets the id slot
signature(object = "Layout"): gets the additionalGraphicalObjects slot
signature(object = "Layout"): sets the additionalGraphicalObjects slot
signature(object = "Layout"): gets the compartmentGlyphs slot
signature(object = "Layout"): sets the compartmentGlyphs slot
signature(object = "Layout"): gets the dimensions slot
signature(object = "Layout"): sets the dimensions slot
signature(object = "Layout"): gets the reactionGlyphs slot
signature(object = "Layout"): sets the reactionGlyphs slot
signature(object = "Layout"): gets the speciesGlyphs slot
signature(object = "Layout"): sets the speciesGlyphs slot
signature(object = "Layout"): gets the textGlyphs slot
signature(object = "Layout"): sets the textGlyphs slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Describes a simple A-B line.
Objects can be created by calls of the form new("LineSegment", ...).
start:Object of class "Point" indicating the start position.
end:Object of class "Point" indicating the end position.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(x = "LineSegment"): ...
signature(object = "LineSegment"): sets the end slot
signature(x = "LineSegment"): ...
signature(object = "LineSegment"): sets the start slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Each of these functions implements a trigonometry function found in the MathML specification but not found in base R. These are all simple wrappers around existing R trig functions.
acot(x) acoth(x) acsc(x) acsch(x) asec(x) asech(x) cot(x) coth(x) csc(x) csch(x) sec(x) sech(x)acot(x) acoth(x) acsc(x) acsch(x) asec(x) asech(x) cot(x) coth(x) csc(x) csch(x) sec(x) sech(x)
x |
The |
A numeric vector, the same length as x.
Michael Lawrence
The central SBML element. Contains the Species,
Reactions, Compartments and other
components of the model. See the SBML specification, at the reference, for
further details.
Objects can be created by calls of the form new("Model", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
functionDefinitions:Object of class "list" containing
FunctionDefinitions. The names of the list
correspond to the IDs of the elements.
unitDefinitions:Object of class "list" containing
UnitDefinitions. The names of the list
correspond to the IDs of the elements.
compartments:Object of class "list" containing
Compartments. The names of the list
correspond to the IDs of the elements.
species:Object of class "list" containing
Speciess. The names of the list
correspond to the IDs of the elements.
parameters:Object of class "list" containing
Parameters. The names of the list
correspond to the IDs of the elements.
rules:Object of class "list" containing
Rules.
reactions:Object of class "list" containing
Reactions. The names of the list
correspond to the IDs of the elements.
events:Object of class "list" containing
Events. The names of the list
correspond to the IDs of the elements.
layouts:Object of class "list" containing
Layouts. The names of the list
correspond to the IDs of the elements.
speciesTypes:Object of class "list" containing
SpeciesTypes. The names of the list
correspond to the IDs of the elements.
compartmentTypes:Object of class "list" containing
CompartmentTypes. The names of the list
correspond to the IDs of the elements.
constraints:Object of class "list" containing
Constraints. The names of the list
correspond to the IDs of the elements.
initialAssignments:Object of class "list" containing
InitialAssignments.
modelHistory:Object of class
ModelHistory recording the history of the
model.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Model"): gets the id slot
signature(object = "Model"): sets the id slot
signature(object = "Model"): gets the name slot
signature(object = "Model"): sets the name slot
signature(object = "Model"): gets the compartments slot
signature(object = "Model"): sets the compartments slot
signature(object = "Model"): gets the events slot
signature(object = "Model"): sets the events slot
signature(object = "Model"): gets the functionDefinitions slot
signature(object = "Model"): sets the functionDefinitions slot
signature(object = "Model"): gets the layouts slot
signature(object = "Model"): sets the layouts slot
signature(object = "Model"): gets the parameters slot
signature(object = "Model"): sets the parameters slot
signature(object = "Model"): gets the species slot
signature(object = "Model"): sets the species slot
signature(object = "Model"): gets the reactions slot
signature(object = "Model"): sets the reactions slot
signature(object = "Model"): gets the rules slot
signature(object = "Model"): sets the rules slot
signature(object = "Model"): gets the unitDefinitions slot
signature(object = "Model"): sets the unitDefinitions slot
signature(object = "Model"): gets the compartmentTypes slot
signature(object = "Model"): sets the compartmentTypes slot
signature(object = "Model"): gets the constraints slot
signature(object = "Model"): sets the constraints slot
signature(object = "Model"): gets the initialAssignments slot
signature(object = "Model"): sets the initialAssignments slot
signature(object = "Model"): gets the speciesTypes slot
signature(object = "Model"): sets the
speciesTypesslot
signature(object = "Model"): gets the modelHistory slot
signature(object = "Model"): sets the modelHistory slot
signature(object = "Model"):
calculates the stoichiometry matrix of the model
Michael Lawrence
Information, such as name, email and organization, about a creator of an SBML model.
Objects can be created by calls of the form new("ModelCreator", ...).
familyName:Object of class "character" specifying
the family name of the creator.
givenName:Object of class "character" specifying
the given name of the creator.
email:Object of class "character" specifying
the email address of the creator.
organization:Object of class "character"
specifying the name of the organization to which the creator belongs.
signature(object = "ModelCreator"): gets the email slot.
signature(object = "ModelCreator"): sets the email<- slot.
signature(object = "ModelCreator"): gets the familyName slot.
signature(object = "ModelCreator"): sets the familyName<- slot.
signature(object = "ModelCreator"): gets the givenName slot.
signature(object = "ModelCreator"): sets the givenName<- slot.
signature(object = "ModelCreator"): gets the organization slot.
signature(object = "ModelCreator"): sets the organization<- slot.
Michael Lawrence
Stores the history of an SBML model, including the created/modified dates and the creators.
Objects can be created by calls of the form new("ModelHistory", ...).
createdDate:Object of class "character"
representing the date/time of creation, in W3CDTF format:
YYYY-MM-DDThh:mm:ssTZD, e.g. "1997-07-16T19:20:30+01:00".
modifiedDate:Object of class "character"
representing the date/time of last modification, in W3CDTF format:
YYYY-MM-DDThh:mm:ssTZD, e.g. "1997-07-16T19:20:30+01:00".
creators:Object of class "list" of instances
of ModelCreator, one for each creator of the model.
signature(object = "ModelHistory"):
get the createdDate slot.
signature(object = "ModelHistory", value =
"character"): Set the createdDate slot to a correctly
formatted string.
signature(object = "ModelHistory", value =
"POSIXt"): Set the createdDate slot with a
POSIXt instance, obtained e.g. from
Sys.time.
signature(object = "ModelHistory"): gets the
creators slot.
signature(object = "ModelHistory"): sets
the creators slot.
signature(object = "ModelHistory"):
get the modifiedDate slot.
signature(object = "ModelHistory", value =
"character"): Set the modifiedDate slot to a correctly
formatted string.
signature(object = "ModelHistory", value =
"POSIXt"): Set the modifiedDate slot with a
POSIXt instance, obtained e.g. from
Sys.time.
Michael Lawrence
Identifies a Species that modifies the parent
Reaction.
Objects can be created by calls of the form new("ModifierSpeciesReference", ...).
id:Object of class "character" uniquely identifying this component.
species:Object of class "character" identifying the
Species being referenced.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SimpleSpeciesReference", directly.
Class "SBase", by class "SimpleSpeciesReference", distance 2.
No methods defined with class "ModifierSpeciesReference" in the signature.
Michael Lawrence
Declares a variable to be used in a mathematical expression.
Objects can be created by calls of the form new("Parameter", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
value:Object of class "numeric" specifying the initial value.
units:Object of class "character" identifying the units.
constant:Object of class "logical" indicating whether
the value of this parameter is constant.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Parameter"): gets the id slot
signature(object = "Parameter"): sets the id slot
signature(object = "Parameter"): gets the name slot
signature(object = "Parameter"): sets the name slot
signature(object = "Parameter"): gets the units slot
signature(object = "Parameter"): sets the units slot
signature(object = "Parameter"): gets the constant slot
signature(object = "Parameter"): sets the constant slot
signature(object = "Parameter"): gets the value slot
signature(object = "Parameter"): sets the value slot
Michael Lawrence
Obsolete rule that controls the value of a Parameter.
Objects can be created by calls of the form new("ParameterRule", ...).
name:Object of class "character" naming this component.
units:Object of class "character" identifying the units
of the assigned value.
variable:Object of class "character", ignored.
type:Object of class "character", deprecated.
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "AssignmentRule", directly.
Class "Rule", by class "AssignmentRule", distance 2.
Class "SBase", by class "AssignmentRule", distance 3.
signature(object = "Parameter"): gets the name slot
signature(object = "Parameter"): sets the name slot
signature(object = "Parameter"): gets the units slot
signature(object = "Parameter"): sets the units slot
signature(object = "Parameter"): gets the variable slot
signature(object = "Parameter"): sets the variable slot
signature(object = "Parameter"): gets the type slot
signature(object = "Parameter"): sets the type slot
signature(object = "Parameter"): gets the math slot
signature(object = "Parameter"): sets the math slot
Michael Lawrence
Specifies a position in 3D space.
Objects can be created by calls of the form new("Point", ...).
x:Object of class "numeric" indicating the X coordinate
y:Object of class "numeric" indicating the Y coordinate
z:Object of class "numeric" indicating the Z coordinate
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Point"): gets the x slot
signature(object = "Point"): sets the x slot
signature(object = "Point"): gets the y slot
signature(object = "Point"): sets the y slot
signature(object = "Point"): gets the z slot
signature(object = "Point"): sets the z slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
An equation that describes the rate of change in the quantity of a
Species, the size of a Compartment
or the value of a Parameter.
Objects can be created by calls of the form new("RateRule", ...).
variable:Object of class "character" naming the
variable (the id of a Species, Compartment
or Parameter) being described.
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "Rule", directly.
Class "SBase", by class "Rule", distance 2.
signature(object = "RateRule"): gets the variable slot
signature(object = "RateRule"): sets the variable slot
Michael Lawrence
Any transformation, transportation or binding process that changes the
quantity of one or more Species.
Objects can be created by calls of the form new("Reaction", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
reactants:Object of class "list" containing
SpeciesReferences specifying the
Species that are reactants for this
reaction. The names of the list correspond to the IDs of the
species.
products:Object of class "list" containing
SpeciesReferences specifying the
Species that are products for this
reaction. The names of the list correspond to the IDs of the
species.
modifiers:Object of class "list" containing
ModifierSpeciesReferences specifying the
Species that are modifiers for this
reaction. The names of the list correspond to the IDs of the
species.
kineticLaw:Object of class "KineticLaw" that dynamically
defines the rate of the reaction.
reversible:Object of class "logical" indicating whether
the direction of this reaction is reversible.
fast:Object of class "logical" indicating whether
this reaction should be considered instantaneous relative to non-fast reactions.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Reaction"): gets the id slot
signature(object = "Reaction"): sets the id slot
signature(object = "Reaction"): gets the name slot
signature(object = "Reaction"): sets the name slot
signature(object = "Reaction"): gets the fast slot
signature(object = "Reaction"): sets the fast slot
signature(object = "Reaction"): gets the kineticLaw slot
signature(object = "Reaction"): sets the kineticLaw slot
signature(object = "Reaction"): gets the modifiers slot
signature(object = "Reaction"): sets the modifiers slot
signature(object = "Reaction"): gets the products slot
signature(object = "Reaction"): sets the products slot
signature(object = "Reaction"): gets the reactants slot
signature(object = "Reaction"): sets the reactants slot
signature(object = "Reaction"): gets the reversible slot
signature(object = "Reaction"): sets the reversible slot
Michael Lawrence
A glyph representing a Reaction in the SBML layout.
Objects can be created by calls of the form new("ReactionGlyph", ...).
reaction:Object of class "character" identifying the reaction
represented by this glyph.
glyphCurve:Object of class "Curve" describing
this glyph as a curve (optional).
speciesReferenceGlyphs:Object of class "list" containing
SpeciesReferenceGlyphs that represent the
SpeciesReferences of the
underlying Reaction. The names of the list
correspond to the IDs of the elements.
id:Object of class "character" uniquely identifying this component.
boundingBox:Object of class "BoundingBox" describing
the position and size of the graphical object.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "GraphicalObject", directly.
Class "SBase", by class "GraphicalObject", distance 2.
signature(expr = "ReactionGlyph"): gets the
glyphCurve slot
signature(object = "ReactionGlyph"): sets the glyphCurve slot
signature(object = "ReactionGlyph"): gets the reaction slot
signature(object = "ReactionGlyph"): sets the reaction slot
signature(object = "ReactionGlyph"): gets the speciesReferenceGlyphs slot
signature(object = "ReactionGlyph"): sets the speciesReferenceGlyphs slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
A mathematical equation.
A virtual Class: No objects may be created from it.
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Rule"): gets the math slot
signature(object = "Rule"): sets the math slot
Michael Lawrence
The abstract type from which all other SBML types are derived.
A virtual Class: No objects may be created from it.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
signature(object = "SBase"): gets the annotation slot
signature(object = "SBase"): sets the annotation slot
signature(object = "SBase"): gets the metaId slot
signature(object = "SBase"): sets the metaId slot
signature(object = "SBase"): gets the notes slot
signature(object = "SBase"): sets the
notesslot
signature(object = "SBase"): gets the
cvTerms slot.
signature(object = "SBase"): sets the
cvTerms slot.
signature(object = "SBase"): gets the
sboTerm slot.
signature(object = "SBase"): sets the
sboTerm slot.
Michael Lawrence
Read an SBML file into R.
rsbml_read(filename, text, dom = TRUE, strict = FALSE, schema = FALSE, consistency = TRUE)rsbml_read(filename, text, dom = TRUE, strict = FALSE, schema = FALSE, consistency = TRUE)
filename |
the name of the SBML file to parse |
text |
a string of SBML text to parse (instead of file) |
dom |
whether to convert directly to the S4 DOM ( |
strict |
whether to report warnings in addition to
errors or not ( |
schema |
whether to perform XML schema validation |
consistency |
whether to perform consistency checks; recommended but might cause performance deficiencies. |
a SBML object, or a
SBMLDocument if dom is FALSE.
Michael Lawrence
# Read an SBML file file <- system.file("sbml", "GlycolysisLayout.xml", package = "rsbml") doc <- rsbml_read(file) # Read an SBML string string <- paste(readLines(file),collapse="\n") doc <- rsbml_read(text = string)# Read an SBML file file <- system.file("sbml", "GlycolysisLayout.xml", package = "rsbml") doc <- rsbml_read(file) # Read an SBML string string <- paste(readLines(file),collapse="\n") doc <- rsbml_read(text = string)
The root element of an SBML document. An actual SBML
Model may be retrieved from an instance of this class.
Objects can be created by calls of the form new("SBML", ...).
level:Object of class "integer" indicating the
level of the SBML standard (currently at 2).
ver:Object of class "integer" indicating the
version of the level (currently at 2 for level 2).
model:Object of class "Model" the SBML model itself.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(from = "SBMLDocument", to = "SBML"):
constructs the S4 object model from a low-level libsbml document.
signature(from = "SBML", to = "SBMLDocument"):
converts the S4 object model to a low-level libsbml document.
signature(from = "SBML", to = "graph"):
converts the S4 object model to a graph.
signature(object = "SBML"): gets the level slot
signature(object = "SBML"): sets the level slot
signature(object = "SBML"): gets the model slot
signature(object = "SBML"): sets the model slot
signature(model = "SBML"): converts the S4 object model
to a low-level libsbml document.
signature(object = "SBML"): writes this document
to a file as SBML.
signature(object = "SBML"): converts this document
to a string as SBML.
signature(object = "SBML"): converts this
document to a graph object.
signature(object = "SBML"): perform
consistency checks, see rsbml_check.
signature(object = "SBML"): converts this
document to an internal SBMLDocument and
calls simulate on it.
signature(object = "SBML"): gets the ver slot
signature(object = "SBML"): sets the ver
slot
Michael Lawrence
# Get a DOM dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml")) # Get the species ID's sapply(species(model(dom)), id) # Convert DOM back to a low-level document for checking doc <- rsbml_doc(dom) rsbml_check(doc) # Write a DOM to a file ## Not run: rsbml_write(dom, "my.xml")# Get a DOM dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml")) # Get the species ID's sapply(species(model(dom)), id) # Convert DOM back to a low-level document for checking doc <- rsbml_doc(dom) rsbml_check(doc) # Write a DOM to a file ## Not run: rsbml_write(dom, "my.xml")
Low-level libsbml document structure.
A virtual Class: No objects may be created from it.
Class "oldClass", directly.
signature(object = "SBMLDocument"):
rsbml_check(object, strict = FALSE, consistency = TRUE):
Check for problems with the document and signal R conditions if
any errors are detected. If strict is
TRUE, libsbml warnings will be emitted as R warnings
(these are often too pedantic). If consistency is
also TRUE, reports problems regarding internal model
inconsistencies. This can be time consuming.
signature(doc = "SBMLDocument"): Constructs an S4
object model from a libsbml document.
signature(doc = "SBMLDocument"): Converts a
libsbml document to a graph.
signature(object = "SBMLDocument"):
reports problems encountered during parsing and/or validation.
signature(object = "SBMLDocument"): writes this
document to a file as SBML.
signature(object = "SBMLDocument"): converts this
document to a string as SBML.
signature(object = "SBMLDocument"):
simulate(object, nsim = 10, seed, ...): a shortcut for
simulating the model in this document using the SBML ODE Solver
library. Arguments in ... should match slots of
SOSProtocol. See simulate for
more details.
Michael Lawrence
# Read a document into an R DOM dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml")) # Convert to a graph graph <- rsbml_graph(dom) # Write it out to a file ## Not run: rsbml_write(dom, "my.xml") # Or convert it to a string of XML rsbml_xml(dom) # Read into external libsbml data structure doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"), dom = FALSE) # Convert it explicitly to an S4 DOM dom <- rsbml_dom(doc)# Read a document into an R DOM dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml")) # Convert to a graph graph <- rsbml_graph(dom) # Write it out to a file ## Not run: rsbml_write(dom, "my.xml") # Or convert it to a string of XML rsbml_xml(dom) # Read into external libsbml data structure doc <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"), dom = FALSE) # Convert it explicitly to an S4 DOM dom <- rsbml_dom(doc)
Represents an exception thrown during SBML parsing.
There are trivial subclasses for fatal errors (SBMLFatal),
recoverable errors (SBMLError), warnings (SBMLWarning)
and informational messages (SBMLInfo). Errors become R
error conditions, warnings become R
warning conditions and messages are output via
message.
line:The "numeric" line number in the SBML
file where the problem was detected.
column:Object of class "numeric" column number
in the SBML file where the problem was detected.
msg:Object of class "character", a
human-readable description of the problem.
signature(object = "SBMLProblem"):
constructs a condition object representing the exception.
Michael Lawrence
SBMLProblems, a container for instances of this class.
A class representing errors encountered during parsing of SBML.
fatals:A list of
SBMLFatal instances.
errors:A list of
SBMLError instances.
warnings:A list of
SBMLWarning instances.
infos:A list of
SBMLInfo instances.
signature(object = "SBMLProblems"): Throws each
SBMLProblem in this object.
signature(object = "SBMLProblems"): Gets the
errors slot.
signature(object = "SBMLProblems"): Gets the
fatals slot.
signature(object = "SBMLProblems"): Gets the
infos slot.
signature(object = "SBMLProblems"): Gets the
warns slot.
Michael Lawrence
The rsbml_problems function for obtaining an instance of this
class describing any problems encountered during parsing.
Base class for bindings between a Species and
a Reaction.
Objects can be created by calls of the form new("SimpleSpeciesReference", ...).
id:Object of class "character" uniquely identifying this component.
species:Object of class "character" identifying the
Species being referenced.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "SpeciesGlyph"): gets the id slot
signature(object = "SpeciesGlyph"): sets the id slot
signature(object = "SpeciesGlyph"): gets the species slot
signature(object = "SpeciesGlyph"): sets the species slot
Michael Lawrence
Specifies the reaction names and their parameter settings
for each run in a batch experiment. It extends matrix; each column
corresponds to a parameter in the model and each row should hold the
parameter settings for one run of the experiment.
It is often desirable to explore the state space of a model by adjusting its initial parameter settings. One could do this by modifying the model itself for each experiment, but this class aims to provide a more convenient and systematic means of running experiments in batch, over a range of parameter settings. The results of the experiment will then contain the output from each run, which may then be compared.
The design is specified as a matrix, and each column in the matrix
should correspond to a parameter defined in an SBML
model. The column names should identify the parameters. These are not
to be confused with the simulation parameters
specified in SOSProtocol, which control how the
simulation is executed. These should be and are designed to be kept
constant across the runs.
There are two different types of parameters: global and local
(reaction) parameters. Global parameters may correspond to a
Species quantity,
Compartment size, or model-level
Parameter value. These should be identified in
the column names by the id of the corresponding SBML
element. The element in the reactions slot for one of these
parameters should be the empty string.
The second type of parameter specifies the value of a
Parameter element within the KineticLaw of a
reaction. These should be named by the id of the
Parameter. They also should be namespaced by the
containing Reaction id, which is stored in the
corresponding element of the reactions slot.
Objects can be created by calls of the form new("SOSDesign", data,
nrow, ncol, byrow, dimnames, ...). This is the same as initializing a
matrix.
.Data:Object of class "matrix", holding the
parameter settings.
reactions:Object of class "character" of
length the number of columns, holding the reaction IDs for
parameters local to a reaction (i.e. KineticLaw
Parameters). For global parameters, the
corresponding value should be the empty string.
Class "matrix", from data part.
Class "ExperimentDesign", directly.
Class "array", by class "matrix", distance 2.
Class "structure", by class "matrix", distance 3.
Class "vector", by class "matrix", distance 4, with explicit coerce.
signature(object = "SOSDesign"): gets the
reactions slot.
signature(object = "SOSDesign"): sets the
reactions slot.
Michael Lawrence
See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.
SOSExperiment, the container of this class, for
configuring and running a simulation.
Implementation of Experiment for
simulating SBML models using the SOS: (S)BML (O)DE (S)olver library.
The general workflow for running a simulation:
Create or import an SBML DOM.
Customize the model, for example by adding perturbation
Events.
Wrap the SBML DOM in a SOSSubject,
e.g. new("SOSSubject", dom).
Optionally construct a SOSDesign for
running the experiment in batch over several sets of model parameter
settings.
Optionally construct a SOSProtocol for
specifying the time points and other parameters controlling the
simulation.
Construct an instance of this class that groups the subject, design and protocol.
Run simulate on the SOSExperiment, optionally
specifying the number of iterations and the random seed.
Analyze the returned SOSResult, perhaps
starting by converting it to a time series with as.ts and
making some plots.
Objects can be created by calls of the form new("SOSExperiment", ...).
protocol:Object of class
SOSProtocol, where
the simulation parameters are specified.
design:Object of class
SOSDesign,
specifying model parameters for each run of a batch experiment.
subject:Object of class SOSSubject,
containing the Model to be simulated.
result:Object of class
SOSResult
containing the result of the simulation.
Class Experiment, directly.
signature(object = "SOSExperiment"):
simulate(object, nsim = 10, seed, ...): Simulates
the SBML document in the subject slot according to the
design points in design and parameters in protocol
for nsim iterations, using seed as the random
seed. Returns an instance of SOSExperiment, which now
should include a SOSResult for analysis.
Michael Lawrence
See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.
The simulate method on SBMLDocument is a
shortcut, but most users will probably find the above approach most
useful.
Holds the parameters controlling the execution of the simulation using the SBML ODE Solver library.
Most users will probably set only the times slot, either
directly or through the timeStep slot and the nsim
parameter to simulate.
Objects can be created by calls of the form new("SOSProtocol",
...). Each argument in ... should correspond to one of the
slots described below.
times:A "numeric" vector indicating the
time points at which to evaluate the model. Defaults to
tail(seq(0, by = timeStep, length.out = nsim + 1),
-1). The model is always evaluated at t = 0. This slot is
ignored when indefinite (below) is TRUE.
timeStep:A scalar "numeric" value, giving the
length in time between model evaluations. This is used when
calculating the default value of times, above, but is
otherwise only relevant when the indefinite slot, below, is
TRUE. Defaults to 1.
indefinite:A scalar "logical", indicating
whether the simulation should run indefinitely, i.e. until one of
the stopping conditions is met. See haltOnEvent and
haltOnSteadyState below. Defaults to FALSE.
atol:Scalar "numeric", the absolute
tolerance in integration error. Defaults to 1e-18.
rtol:Scalar "numeric", the relative tolerance
in integration error. Defaults to 1e-10.
maxStep:Sclar "numeric", the maximum number of
steps for integration. Not to be confused with timeStep, etc,
above, which control the simulation time points. Defaults to
10000.
odeMethod:Scalar "character" naming the
method for solving ODEs. Either "bdf" (the default) or
"adams-moulton".
iterMethod:Scalar "character", naming the
iteration method used by the ODE solver, either "newton"
(the default) or "functional".
maxOrder:Scalar "numeric" indicating maximum
order for the ODE solver. Defaults to 5.
sensMethod:Scalar "character" naming the
method for sensitivity analysis. One of "none" (the
default and currently the only valid option),
"simultaneous", "staggered" or "staggered1".
haltOnEvent:Scalar "logical" indicating
whether the simulation should halt when the model emits an
Event. This allows the model to stop the
simulation when some state is reached. Defaults to FALSE.
haltOnSteadyState:Scalar "logical", indicating
whether to halt when a steady state is detected. Defaults to
FALSE.
useJacobian:Scalar "logical" indicating
whether to use Jacobian ASTs (TRUE, the default) or the
internal approximation in the CVODES library.
storeResults:Scalar "logical" indicating
whether to store the entire time course (TRUE, the default)
or just the last time point. Just for performance.
Class "ExperimentProtocol", directly.
No methods defined with class "SOSProtocol" in the signature.
Michael Lawrence
See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.
The SOSExperiment class, which contains
a SOSProtocol instance, for setting up and running a simulation.
A result from simulating an
SOSExperiment. Contains the time course for each
of the model variables: the Species quantities,
Compartment sizes, Parameter
values, and Reaction rates.
data:A "data.frame" containing the time course
data. Each row contains the value at a single time point for a
single time course. Has the following columns:
sampleA factor, the run number, only exists if there
were multiple runs, see SOSDesign.
typeA factor, the SBML element type for the time course,
e.g. "species".
idA factor, the id of the SBML element for
the time course.
timeThe numeric time value for the time point.
valueThe actual numeric value for the time course at that time.
sens:A "matrix" with results from sensitivity
analysis, not yet supported.
Class "ExperimentResult", directly.
signature(x = "SOSResult"): converts this object
to a time course object of class ts. This allows analysis of
the results with existing R infrastructure for time course analysis.
signature(object = "SOSResult"): returns
a subset containing only the Compartment size
courses.
signature(object = "SOSResult"): returns
a subset containing only the global Parameter
value courses.
signature(object = "SOSResult"): returns
a subset containing only the Reaction rate courses.
signature(object = "SOSResult"): returns
a subset containing only the Species quantity
courses.
Michael Lawrence
See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.
SOSExperiment for running a simulation and
obtaining an instance of this class.
This just marks an SBML object as being a
valid subject for simulation using the SBML ODE Solver library.
Normally created from a SBML with: new("SOSSubject", model).
Class "ExperimentSubject", directly.
Class "SBML", directly.
Class "SBase", by class "SBML", distance 2.
Class "Describable", by class "SBML", distance 3.
Michael Lawrence
See http://www.tbi.univie.ac.at/~raim/odeSolver/ for more information on the SBML ODE Solver library.
SOSExperiment for running a simulation on a
SOSSubject.
A participant in an SBML model.
Objects can be created by calls of the form new("Species", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
compartment:Object of class "character" identifying the
compartment in which this species is located.
initialAmount:Object of class "numeric" indicating the
initial amount for this species (mutually exclusive with initialConcentration).
initialConcentration:Object of class "numeric" indicating the
initial concentration for this species (mutually exclusive with initialAmount).
substanceUnits:Object of class "character" identifying the
units for the amount of this species or the numerator of the concentration.
spatialSizeUnits:Object of class "character" identifying the
units for the denominator of the species concentration.
hasOnlySubstanceUnits:Object of class "logical" indicating
whether the quantity of this species is specified as an amount or a concentration.
boundaryCondition:Object of class "logical". If TRUE,
indicates that the quantity of this species cannot be changed by a reaction.
charge:Object of class "integer" indicating the electrical
charge of this species.
constant:Object of class "logical" indicating whether
the quantity of this species can change.
units:Object of class "character", deprecated.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Species"): gets the id slot
signature(object = "Species"): sets the id slot
signature(object = "Species"): gets the name slot
signature(object = "Species"): sets the name slot
signature(object = "Species"): gets the boundaryCondition slot
signature(object = "Species"): sets the boundaryCondition slot
signature(object = "Species"): gets the charge slot
signature(object = "Species"): sets the charge slot
signature(object = "Species"): gets the compartment slot
signature(object = "Species"): sets the compartment slot
signature(object = "Species"): gets the constant slot
signature(object = "Species"): sets the constant slot
signature(object = "Species"): gets the constant slot
signature(object = "Species"): sets the constant slot
signature(object = "Species"): gets the hasOnlySubstanceUnits slot
signature(object = "Species"): sets the hasOnlySubstanceUnits slot
signature(object = "Species"): gets the initialAmount slot
signature(object = "Species"): sets the initialAmount slot
signature(object = "Species"): gets the initialConcentration slot
signature(object = "Species"): sets the initialConcentration slot
signature(object = "Species"): gets the spatialSizeUnits slot
signature(object = "Species"): sets the spatialSizeUnits slot
signature(object = "Species"): gets the substanceUnits slot
signature(object = "Species"): sets the substanceUnits slot
Michael Lawrence
Obsolete type of rule that describes the concentration of
Species.
Objects can be created by calls of the form new("SpeciesConcentrationRule", ...).
species:Object of class "character" identifying the
Species.
variable:Object of class "character", ignored.
type:Object of class "character", deprecated.
math:Object of class "expression" specifying the equation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "AssignmentRule", directly.
Class "Rule", by class "AssignmentRule", distance 2.
Class "SBase", by class "AssignmentRule", distance 3.
signature(object = "SpeciesConcentrationRule"): gets the species slot
signature(object = "SpeciesConcentrationRule"): sets the species slot
Michael Lawrence
A glyph representing a Species in an SBML layout.
Objects can be created by calls of the form new("SpeciesGlyph", ...).
species:Object of class "character" identifying the species
this glyph represents.
id:Object of class "character" uniquely identifying this component.
boundingBox:Object of class "BoundingBox" describing
the position and size of the graphical object.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "GraphicalObject", directly.
Class "SBase", by class "GraphicalObject", distance 2.
signature(object = "SpeciesGlyph"): gets the species slot
signature(object = "SpeciesGlyph"): sets the species slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Binds a reactant or product Species to
a Reaction.
Objects can be created by calls of the form new("SpeciesReference", ...).
stoichiometry:Object of class "numeric" indicating the
(static) stoichiometric coefficient.
stoichiometryMath:Object of class "StoichiometryMath"
that dynamically calculates the stoichiometric coefficient.
id:Object of class "character" uniquely identifying this component.
species:Object of class "character" identifying the
Species being referenced.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SimpleSpeciesReference", directly.
Class "SBase", by class "SimpleSpeciesReference", distance 2.
signature(object = "SpeciesReference"): gets the stoichiometry slot
signature(object = "SpeciesReference"): sets the stoichiometry slot
signature(object = "SpeciesReference"): gets the stoichiometryMath slot
signature(object = "SpeciesReference"): sets the stoichiometryMath slot
Michael Lawrence
A glyph representing a SpeciesReference in an SBML layout.
Objects can be created by calls of the form new("SpeciesReferenceGlyph", ...).
speciesGlyph:Object of class "character" identifying
the SpeciesGlyph representing the Species
that is referenced by the underyling SpeciesReference.
speciesReference:Object of class "character" identifying
the linkS4class{SpeciesReference} represented by this glyph.
role:Object of class "character" indicating how this
glyph should represent the "role" of the underlying SpeciesReference.
glyphCurve:Object of class "Curve" describing
this glyph as a curve (optional).
id:Object of class "character" uniquely identifying this component.
boundingBox:Object of class "BoundingBox" describing
the position and size of the graphical object.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "GraphicalObject", directly.
Class "SBase", by class "GraphicalObject", distance 2.
signature(object = "SpeciesReferenceGlyph"): gets the role slot
signature(object = "SpeciesReferenceGlyph"): sets the role slot
signature(object = "SpeciesReferenceGlyph"): gets the speciesGlyph slot
signature(object = "SpeciesReferenceGlyph"): sets the speciesGlyph slot
signature(object = "SpeciesReferenceGlyph"): gets the speciesReference slot
signature(object = "SpeciesReferenceGlyph"): sets the speciesReference slot
signature(expr = "SpeciesReferenceGlyph"):
gets the glyphCurve slot
signature(object = "SpeciesReferenceGlyph"): sets the glyphCurve slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
A Species represents a pool of a chemical
in a particular linkS4class{Compartment}. This element specifies a
type of species, that is, the chemical independent of location.
Objects can be created by calls of the form new("SpeciesType", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "SpeciesType"): gets the id slot
signature(object = "SpeciesType"): sets the id slot
signature(object = "SpeciesType"): gets the name slot
signature(object = "SpeciesType"): sets the name slot
Requires libsbml >= 3.0
Michael Lawrence
Dynamically defines the stoichiometry of a SpeciesReference.
Objects can be created by calls of the form new("StoichiometryMath", ...).
math:Object of class "expression" that evaluates to
the stoichiometric coefficient.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "StoichiometryMath"): gets the math slot
signature(object = "StoichiometryMath"): sets the math slot
Michael Lawrence
A run of text in an SBML layout.
Objects can be created by calls of the form new("TextGlyph", ...).
graphicalObject:Object of class "character" identifying
the GraphicalObject that this glyph labels (optional).
text:Object of class "character" containing the text
shown by the glyph (mutually exclusive with originOfText).
originOfText:Object of class "character" identifying
an SBML component whose name is used as the text (mutually exclusive with text).
id:Object of class "character" uniquely identifying this component.
boundingBox:Object of class "BoundingBox" describing
the position and size of the graphical object.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "GraphicalObject", directly.
Class "SBase", by class "GraphicalObject", distance 2.
signature(object = "TextGlyph"): gets the graphicalObject slot
signature(object = "TextGlyph"): sets the graphicalObject slot
signature(object = "TextGlyph"): gets the originOfText slot
signature(object = "TextGlyph"): sets the originOfText slot
signature(x = "TextGlyph"): ...
signature(object = "TextGlyph"): sets the text slot
Michael Lawrence
http://projects.villa-bosch.de/bcb/sbml
Expresses when an Event should be fired.
Objects can be created by calls of the form new("Trigger", ...).
math:Object of class "expression" that evaluates to
TRUE when the event should be fired.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(domain = "Trigger"): gets the math slot.
signature(object = "Trigger"): sets the
math slot.
Requires libsbml >= 3.0
Michael Lawrence
Event, the parent of this element.
A (possibly transformed) reference to a base UnitKind. The
transformation is of the form: $multiplier * 10^scale * x^exponent + offset$.
Objects can be created by calls of the form new("Unit", ...).
kind:Object of class "character" identifying a
an SBML UnitKind. For possible values see Table 2 in the SBML specification.
exponent:Object of class "integer" indicating the
exponent to use in the transformation.
unitScale:Object of class "integer" indicating the
order of magnitude of the scaling to use in the transformation.
multiplier:Object of class "numeric" indicating
the factor to use for scaling in the transformation.
offset:Object of class "numeric" indicating the
amount of constant shift in the transformation.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "Unit"): gets the exponent slot
signature(object = "Unit"): sets the exponent slot
signature(object = "Unit"): gets the kind slot
signature(object = "Unit"): sets the kind slot
signature(object = "Unit"): gets the multiplier slot
signature(object = "Unit"): sets the multiplier slot
signature(object = "Unit"): gets the offset slot
signature(object = "Unit"): sets the offset slot
signature(x = "Unit"): ...
signature(object = "Unit"): sets the unitScale slot
Michael Lawrence
Associates one or more Units with an ID and name.
Objects can be created by calls of the form new("UnitDefinition", ...).
id:Object of class "character" uniquely identifying this component.
name:Object of class "character" naming this component.
units:Object of class "list" containing equivalent
Units that are all associated with the same ID and name.
metaId:Object of class "character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element.
notes:Object of class "character"
containing user-readable XHTML notes about an element.
annotation:Object of class "character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs.
cvTerms:Object of class "list" containing
instances of CVTerm associated with this
element.
sboTerm:Object of class "integer" identifying
a term in the Systems Biology Ontology (SBO).
Class "SBase", directly.
signature(object = "UnitDefinition"): gets the id slot
signature(object = "UnitDefinition"): sets the id slot
signature(object = "UnitDefinition"): gets the name slot
signature(object = "UnitDefinition"): sets the name slot
signature(object = "UnitDefinition"): gets the units slot
signature(object = "UnitDefinition"): sets the units slot
Michael Lawrence