File: User.htd

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<html>
<head>
<title>User's Guide</title>
</head>
<body>
<h1>User's Guide</h1>

<p>
The application window is composed of twelve panels and a toolbar. The
panels are labeled in the figure below. These will each be described
in turn. If you pause the cursor over a title in any of the panels in
the application window you will see a tool tip that describes the
relevant functionality.
</p>

<p align="center">
<img src="CainCapture.png">
</p>

<p>
The six panels in the top row follow the workflow of running a stochastic
simulation. Select a model (a system of species and the reactions that govern
their evolution) in the model list. Then select a simulation method. One can
use exact or approximate methods to generate realizations of the process.
In the recorder panel you specify the species and reactions that you want to
record. In the launcher panel you select the number of trajectories to generate
and start the simulation. The simulation output is listed in the rightmost
panel.
</p>

<p>
The six panels in the bottom two rows comprise the model editor. These show the
species, reactions, compartments, time events, trigger events, and
parameters for the selected model. If nothing
is selected in the model list panel, the model editor panels are
empty. You can edit a model via the grids and their toolbars in each panel.
</p>

</body>
</html>