File: Faq.htm

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

<p>
<b>Why is this program called Cain?</b><br>
I couldn't think of a Catchy And Informative Name.
</p>

<p>
<b>Where can I get the latest version of Cain?</b><br>
<a href="http://cain.sourceforge.net/">http://cain.sourceforge.net/</a>
</p>

<p>
<b>How can I cite Cain?</b>
Please cite reference [<a href="Bibliography.htm#mauch2011">Mauch 2011</a>].
</p>

<p>
<b>I found an error. What should I do?</b><br>
Don't panic! Send an email to <img src="seanEmail.png">.  Please include
any relevant data files and a description of what causes the problem.
Check the <tt>.cain</tt> directory in your home directory. 
If Cain wrote a file called <tt>ErrorLog.txt</tt> there,
include that as well.
</p>

<p>
<b>I have a question or feature request. Who should I contact?</b><br>
<img src="seanEmail.png">
</p>

<p>
<b>Why can't I add species, reactions, etc. to a blank model?</b><br>
You must add a model in the models list (upper left panel) before you
define the species, reactions, etc. that define it. Note that if no
model is selected in the models list, then the buttons which add, delete,
move, and sort the models elements are disabled.
</p>

<p>
<b>Why can't I edit the model or the method?</b><br>
You have generated output using that model or that method.  Once you
have done this, Cain will not let you modify them. If it did, the
model or method would no longer correspond to the generated output. If
you delete the output you will be able to edit the model or method.
If you want to keep the output, clone the model or method.
</p>

<p>
<b>The simulation completes, but why are there no
trajectories?</b><br>
If all of the simulations fail, then no trajectories will be
generated. The completion window will indicate how many trajectories
were successfully generated and how many failed. One of the common
causes of failure is exceeding the maximum number of allowed steps. If
this is the case, try leaving the &quot;Maximum steps&quot; field
blank in the method editor. (Alternatively, you may enter a sufficiently
large value.) If you are using an approximate method like tau-leaping
a simulation may fail if a species population becomes negative. In
this case, try reducing the error tolerance or the step size.
</p>

</body>
</html>