As mentioned previously, the block diagram representation of the system is made up of various type of icons. Basically, one has to specify the model of the system (state space, discrete, transfer functions, nonlinear ODE's, etc), the input (source) to the system, and where the output (sink) of the simulation of the system will go. Open up the Sources, Sinks, and Linear windows by clicking on the appropriate icons. Note the different types of sources (step function, sinusoidal, white noise, etc.), sinks (scope, file, workspace), and linear systems (transfer function, state space model, etc.).
For example, you may be interested in simulating a step input to a first-order transfer function in the Laplace domain and viewing the result graphically in MATLAB. The resulting block diagram is shown in Figure 3. To do this, you would "drag" a step function icon from the Sources window, a transfer function icon from the Linear window, two to workspace icons from the Sinks window, and a clock icon from the Source window to the blank block diagram window.
The next step is to connect these icons together by drawing lines connecting the icons using the left-most mouse button (hold the button down and drag the mouse to draw a line). Connect the step function icon to the input of the transfer function icon, then connect the output of the transfer function icon to first to workspace icon. Then, connect the clock icon to the second to workspace icon. ``Open'' the icons (by double clicking on them with the left-most mouse button) and set the values of the various parameters; for example the step size and step time in the step function icon, the transfer function coefficients in the transfer function icon, and the variable names in the to workspace icons (generally, the clock variable is denote as time, whereas the output variable is denoted y). Select the parameter field from the simulation menu (in the block diagram window) and set the proper integration details (min and max stepsizes, start and stop integration times, integration code, etc.). Finally, select start from the simulation menu to start the simulation. The output of the simulation will be sent to the MATLAB command line interface (CLI) (aka the MATLAB prompt, >>). The result can be plotted as one would normally plot ( e.g. plot(time,y) ), since the variables time and y are now defined in the MATLAB workspace. The result is shown in Figure 4, for a first-order transfer function with a time constant = 2, and a unit step input at time = 1.