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Tim Vaughan edited this page Mar 17, 2015 · 4 revisions

The <model> element specifies the birth-death model that MASTER will simulate. It has the following basic structure:

    <model spec='Model'>
      <!-- Populations and/or Population Types -->
      <!-- Reaction Groups and/or Reactions -->
      <!-- Functions -->
    </model>

Firstly, the model consists of elements defining the population types constituting the system state. These can be specified directly via one or more populationType elements, or specified using the type corresponding to a particular population element. The second approach makes specification easier when the population is unstructured.

Secondly, the model consists of elements defining the reactions under which the system state will evolve. These reactions may be grouped into logical reactionGroup elements, or specified individually using reaction elements.

Finally, the model may contain zero or more function elements which allow for user-defined functions to be specified for use in rateMultiplier or predicate expressions.

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