Dynamics

Generated on 22/08/23. Please file any issues or questions at the issue tracker here.

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Dynamics

Specifies the dynamical behavior of components build from this ComponentType. Note that all variables in a Dynamics definition are private. If other components need access to them, then the definition should explicitly link them to an Exposure defined in the component class

can contain these elements

supers	Super
derivedVariables	DerivedVariable
conditionalDerivedVariables	ConditionalDerivedVariable
stateVariables	StateVariable
timeDerivatives	TimeDerivative
kineticSchemes	KineticScheme
onStarts	OnStart
onEvents	OnEvent
onConditions	OnCondition
stateScalarFields	StateScalarField
derivedScalarFields	DerivedScalarField
derivedPunctateFields	DerivedPunctateField
regimes	Regime

StateVariable

Properties

name	String	Name of the state variable
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
exposure	String	If this variable is to be accessed from outside, it should be linked to an Exposure that is defined in the ComponentType.
description	String	An optional description of the state variable

StateAssignment

Has ‘variable’ and ‘value’ fields

Properties

variable	String	The name of the variable
value	String	A string defining the value of the element

TimeDerivative

First order differential equations, functions of StateVariables and Parameters, for how StateVariables change with time. Has a variable and a value. The value is the rate of change of the variable.

Properties

variable	String	The name of the variable
value	String	A string defining the value of the element

DerivedVariable

A quantity that depends algebraically on other quantities in the model. The ‘value’ field can be set to a mathematical expression, or the ‘select’ field to a path expression. If the path expression produces multiple matches, then the ‘reduce’ field says how these are reduced to a single value by taking the sum or product.

Properties

name	String	Name of the derived variable
select	String	A path to the variable that supplies the value. Note that to select a variable from another component, the variable must be marked as an Exposure. Exactly one of ‘select’ and ‘value’ is required
dimension	String	The dimension, or ‘none’. This should be the name of an already defined dimension element
description	String	An optional description of the derived variable
reduce	String	Either ‘add’ or ‘multiply’. This applies if ther are multiple matches to the path or if ‘required’ is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to ‘add’ then additive expressions behave as if it was not there and multiplicative ones generateand error.
exposure	String
required	boolean	Set to true if it OK for this variable to be absent. See ‘reduce’ for what happens in this case
value	String	A string defining the value of the element

OnStart

can contain these elements

stateAssignments	StateAssignment
eventOuts	EventOut
transitions	Transition

OnCondition

can contain these elements

stateAssignments	StateAssignment
eventOuts	EventOut
transitions	Transition

OnEvent

Event handler block

Properties

port

String

the port to listen on

can contain these elements

stateAssignments	StateAssignment
eventOuts	EventOut
transitions	Transition

EventOut

KineticScheme

Allows the specification of systems that can be in one of a small number of states at any time with probabilistic transitions between states. This includes continuous time Markov processes as are used for stochastic models of ion channels. A kinetic scheme does not itself introduce any new elements or state variables. It is rather a way of connecting quantities in existing components by saying that quantities in the edge elements should be interpreted as transition rates among quantities in the node elements.

Properties

name	String	Name of kinetic scheme
nodes	String	Source of notes for scheme
edges	String	The element that provides the transitions for the scheme
stateVariable	String	Name of state variable in state elements
edgeSource	String	The name of the attribute in the rate element that defines the source of the transition
edgeTarget	String	Attribute tha defines the target
forwardRate	String	Name of forward rate exposure
reverseRate	String	Name of reverse rate exposure

Regime

Allows the dynamics of a ComponentType to be expressed via a finite state machine. Each regime has its internal dynamics, and conditions on which transitions between regimes occur are specified using the OnCondition element

Properties

name	String	The name of the regime
initial	String	‘True’ if this is the initial regime of the system

can contain these elements

derivedVariables	DerivedVariable
stateVariables	StateVariable
timeDerivatives	TimeDerivative
onStarts	OnStart
onEntrys	OnEntry
onEvents	OnEvent
onConditions	OnCondition
requiredVars	lemsschema:requiredvar_

OnEntry

can contain these elements

stateAssignments	StateAssignment
eventOuts	EventOut
transitions	Transition

Transition

Super

ConditionalDerivedVariable

Properties

name	String
dimension	String
exposure	String

can contain these elements

cases

Case

Case

Properties

value

String

A string defining the value of the element

Equilibrium

can contain these elements

derivedVariables

DerivedVariable

StateScalarField

DerivedScalarField

DerivedPunctateField