readme-sbml-annotation.md

#Spatial SBML Settings The SpatialUI application uses a custom SBML annotation of the SBML Model element, to store the initial setup of a loaded spatial model. The format looks like this:

  <spatialInfo xmlns="http://fbergmann.github.io/spatial-sbml/settings">
    <update step="0.00001" freq="100"/>
    <items>
      <item sbmlId="p65_P_cytoplasm" palette="black-blue.txt" max="0.001"/>
	  ...
    </items>
  </spatialInfo>

and is described in more detail below.

The Update Element

The update element holds two attributes:

• step of type double describes the initial step size used for the model, and is to be chosen such that the integrator should not fall over immidiately.
• freq of type int describes how often the application should attempt to render the scene.

The item element

The item element also consists of three elements:

• sbmlId of type string is the id of a spatial species to be visualized.
• palette of type string is the name of a palette to be used. It should be the value of one of the palettes distributed (and present) with SpatialUI
• max of type double is then the maximum value the species will take during the simulation. The values of the palette chosen will be scaled from [0...max] and assign 0 the min value of the palette, and max accordingly the highest value.