File: XmlModels.htd

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<html>
<head>
<title>Models</title>
</head>
<body>
<h1>Models</h1>

<p>
The model element is just a simplified version of its SBML counterpart.
However, in an SBML file there is a single model element. Cain files can
have any number of models. Below is the top-level structure.
</p>

<pre>  &lt;model id=&quot;Identifier&quot; <font color="#777777">name=&quot;String&quot;</font>&gt;
    <font color="#777777">&lt;listOfParameters&gt;
      <em>One or more</em> &lt;parameter&gt; <em>elements.</em>
    &lt;/listOfParameters&gt;
    &lt;listOfCompartments&gt;
      <em>One or more</em> &lt;compartment&gt; <em>elements.</em>
    &lt;/listOfCompartments&gt;</font>
    &lt;listOfSpecies&gt;
      <em>One or more</em> &lt;species&gt; <em>elements.</em>
    &lt;/listOfSpecies&gt;
    <font color="#777777">&lt;listOfReactions&gt;
      <em>One or more</em> &lt;reaction&gt; <em>elements.</em>
    &lt;/listOfReactions&gt;
    &lt;listOfTimeEvents&gt;
      <em>One or more</em> &lt;timeEvent&gt; <em>elements.</em>
    &lt;/listOfTimeEvents&gt;
    &lt;listOfTriggerEvents&gt;
      <em>One or more</em> &lt;triggerEvent&gt; <em>elements.</em>
    &lt;/listOfTriggerEvents&gt;</font>
  &lt;/model&gt;</pre>

<p>
<a href="UserParameter.htm">Parameters</a> are Python expressions which may use mathematical functions and
other parameter identifiers. Parameters must evaluate to a numerical
value; functions of time are not allowed.
</p>

<pre>  &lt;parameter id=&quot;Identifier&quot; expression=&quot;PythonExpression&quot; <font color="#777777">name=&quot;String&quot;</font>/&gt;</pre>

<p>
<a href="UserCompartment.htm">Compartments</a> are only used for information. They do not affect simulation
output.
</p>

<pre>  &lt;compartment id=&quot;Identifier&quot; <font color="#777777">name=&quot;String&quot; spatialDimensions=&quot;Dimension&quot;
   size=&quot;Number&quot; constant=&quot;Boolean&quot; outside=&quot;Identifier&quot;</font>/&gt;</pre>

<p>
The initial amount of a <a href="UserSpecies.htm">species</a> must evaluate to a non-negative integer.
</p>

<pre>  &lt;species id=&quot;Identifier&quot; initialAmount=&quot;PythonExpression&quot; <font color="#777777">name=&quot;String&quot; compartment=&quot;Identifier&quot;</font>/&gt;</pre>

<p>
The <a href="UserReaction.htm">reaction</a>
element is simpler than its SBML counterpart. There is no
reversible attribute. In stochastic simulations one represents a
reversible reaction by specifying both the forward and backward
reactions along with their kinetic laws. Note that while the
listOfReactants and listOfProducts elements are optional, at least one
of the two must be present.  Instead of containing a kineticLaw
element, the reaction element has the propensity attribute. For
mass-action kinetics, the propensity is a python expression.
</p>

<pre>  &lt;reaction id=&quot;Identifier&quot; massAction=&quot;true&quot; propensity=&quot;PythonExpression&quot; <font color="#777777">name=&quot;String&quot;</font>&gt;
    <font color="#777777">&lt;listOfReactants&gt;
      <em>One or more</em> &lt;speciesReference&gt; <em>elements.</em>
    &lt;/listOfReactants&gt;
    &lt;listOfProducts&gt;
      <em>One or more</em> &lt;speciesReference&gt; <em>elements.</em>
    &lt;/listOfProducts&gt;</font>
  &lt;/reaction&gt;</pre>

<p>
If the reaction does not use a mass-action kinetics law, the propensity
is a C++ expression. (See the
<a href="UserReactions.htm">Reaction Editor</a> section.)
</p>

<pre>  &lt;reaction id=&quot;Identifier&quot; massAction=&quot;false&quot; propensity=&quot;C++Expression&quot; <font color="#777777">name=&quot;String&quot;</font>&gt;
    <font color="#777777">...</font>
  &lt;/reaction&gt;</pre>

<p>
The speciesReference element is used to represent reactants and products.
The stoichiometry attribute must be a positive integer. Omitting it indicates
that the stoichiometry is one.
</p>

<pre>  &lt;speciesReference species=&quot;Identifier&quot; <font color="#777777">stoichiometry=&quot;Integer&quot;</font>/&gt;</pre>


<p>
<a href="UserTimeEvents.htm">Time events</a>
execute assignments at a specified list of times.
</p>

<pre>  &lt;timeEvent id=&quot;Identifier&quot; times=&quot;PythonExpression&quot; assignments=&quot;PythonExpression&quot; <font color="#777777">name=&quot;String&quot;</font>/&gt;</pre>


<p>
<a href="UserTriggerEvents.htm">Trigger events</a>
execute assignments when the trigger condition becomes true. If the
delay is omitted, it has the value zero. That is, there is no delay
between triggering the event and executing the event. If the
useValuesFromTriggerTime attribute is omitted, it is false.
</p>

<pre>  &lt;triggerEvent id=&quot;Identifier&quot; trigger=&quot;PythonExpression&quot; assignments=&quot;PythonExpression&quot; <font color="#777777">delay=&quot;Number&quot; useValuesFromTriggerTime=&quot;Boolean&quot; name=&quot;String&quot;</font>/&gt;</pre>


</body>
</html>