From 270e8acd2a85b28e8e6527a25cbb6cc85b063dcd Mon Sep 17 00:00:00 2001 From: "Frank T. Bergmann" Date: Tue, 24 Jun 2014 10:07:11 +0200 Subject: [PATCH] - added documentation for sbml annotation --- readme-sbml-annotation.md | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 readme-sbml-annotation.md diff --git a/readme-sbml-annotation.md b/readme-sbml-annotation.md new file mode 100644 index 0000000..b1558c5 --- /dev/null +++ b/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: + + + + + + ... + + + +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. +