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<html>
<head>
<title>Cain XML File Format</title>
</head>
<body>
<h1>Cain XML File Format</h1>

<p>
Cain files store the models, methods, simulation output, and random number
states. Below is the overall structure of a Cain file. The required elements
are shown in black; the optional elements are colored grey.
</p>

<pre>  &lt;?xml version=&quot;1.0&quot; encoding=&quot;utf-8&quot;?&gt;
  &lt;cain version=&quot;Number&quot;&gt;<font color="#777777">
    &lt;listOfModels&gt;
      <em>One or more</em> &lt;model&gt; <em>elements.</em>
    &lt;/listOfModels&gt;
    &lt;listOfMethods&gt;
      <em>One or more</em> &lt;method&gt; <em>elements.</em>
    &lt;/listOfMethods&gt;
    &lt;listOfOutput&gt;
      <em>One or more output elements.</em>
    &lt;/listOfOutput&gt;
    &lt;random&gt;
      <em>Zero or more</em> &lt;stateMT19937&gt; <em>elements.</em>
    &lt;/random&gt;</font>
  &lt;/cain&gt;</pre>

<p>
In the next few sections we will describe each of the top-level elements.
Each element attribute has one of the following formats:
<ul>
  <li> An <b>Identifier</b> is a string that starts with an underscore
  or a letter and is composed entirely of underscores, letters and digits. 
  See the <a href="UserSpecies.htm">Species Editor</a> section for details.
  <li> A <b>String</b> is an arbitrary string (sequence of characters). These
  are used for descriptive names.
  <li> <b>Boolean</b> is either &quot;true&quot; or &quot;false&quot;.
  <li> <b>Integer</b> is a 32-bit unsigned integer.
  <li> <b>Number</b> is a floating-point number.
  <li> <b>PythonExpression</b> is a Python expression. If you use functions
  from the math package, don't use the &quot;math.&quot; qualification,
  i.e. write &quot;floor(exp(5))&quot; instead of
  &quot;math.floor(math.exp(5))&quot;. 
  See the discussion of initial amounts in the
  <a href="UserSpecies.htm">Species Editor</a> section for more information.
  <li> <b>C++Expression</b> is a C++ expression.
  See the <a href="UserReactions.htm">Reaction Editor</a> section for details.
</ul>
</p>

</body>
</html>