Inchman SBML Annotations

The current version of SBML does not yet support spatial information. For this reason, Inchman uses an annotated SBML model to convey any spatial and simulation-specific information needed to run the full model. This document lists the available annotations for the various SBML components. All parameters which are given as MathML expressions can make use of the model parameters.

SBML Container

• im:sbml
  • im:solver The solver type. Available types are stochastic_homogeneous, stochastic_inhomogeneous, deterministic_homogeneous and deterministic_inhomogeneous.
  • im:runs The number of runs as a MathML expression.
  • im:time The simulation run time as a MathML expression.
  • im:outputInterval The output interval as a MathML expression.
  • im:init The initialization method.
    • im:script The actual script as a XML CDATA array.
  • im:events The events method.
    • im:script The actual script as a XML CDATA array.
    • im:listOfTimeStamps A list of the time stamps for which the events script is called.
  • im:driftDiffusivity The inhomogeneous drift-diffusivity method. Attributes are nonLinear and computeMoments which can be set to true or false.
    • im:method The actual method as a XML CDATA array.
  • im:setField The update fields method.
    • im:method The actual method as a XML CDATA array.
  • im:newIndividualsMethod The New Individuals Method.
    • im:method The actual method as a XML CDATA array.

Model

• im:model The Inchman model annotations.
  • im:gridWidth The grid width as a MathML expression.
  • im:gridHeight The grid height as a MathML expression.
  • im:physicalWidth The physical width as a MathML expression.
  • im:physicalHeight The physical height as a MathML expression.

Compartment

• im:compartment The Inchman compartment annotations.
  • im:x The compartment position (x) as a MathML expression.
  • im:y The compartment position (y) as a MathML expression.
  • im:width The compartment width as a MathML expression.
  • im:height The compartment height as a MathML expression.

Species

Note

Inchman does not support constraining species to particular compartments. All species have the obligatory World compartment as the associated compartment.

• im:species The Inchman species annotations.
  • im:diffusionConstant The diffusivity of the species as a MathML expression.
  • im:individual If this tag is present, the species is an individual species.
  • im:listOfCompartmentParameters Can be used to specify the initial amount of this species in the compartment
    • im:initialAmount The initial amount of this species in this compartment.

Parameters

Note

Parameters are defined using the SBML parameter tag with the corresponding id. The value tag is ignored and instead the parameter value is set from the information specified in the annotation. The value of field parameters is set in the initialization method.

• im:parameter The Inchman parameter annotations.
  • type This attribute can be set to either int or float
  • domain This attribute can be set to single, range, random or field.
  • from The bottom end of the sweeping range. If the parameter domain is single, this is the value of the parameter.
  • to The top end of the sweeping range.
  • step The step size for the sweeping.
  • points The number of sample points for the sweeping.

Reactions

• im:reaction The Inchman reaction annotations.
  • im:listOfCompartmentParameters Can be used to constrain the reaction to particular compartments.
    • im:compartmentParameters The compartments this reaction is constrained to are given in the attribute compartment
      • im:isAllowed A MathML expression evaluating to either true or false to allow or disallow this reaction in the compartment.