# User's Guide

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.

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.

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.