- added documentation for sbml annotation

readme-sbml-annotation.md

@@ -0,0 +1,26 @@
+#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. 
+