First, define a control loop and use it to generate process data. Start PID Loop Simulator and select New and then Flow. (Flows and similar processes are called First Order Plus Dead Time (FOPDT) non-integrating or self regulating processes.) You will be presented with the following form. To mimic this example, set the simulator's parameters as indicated below.
Click the Run button on the toolbar. After the process variable (PV) stabilizes, perform a series of open loop step tests. Then pause the simulator (or not) and click the chart area to expose the scooters. Position the scooters so they enclose your step tests. Your simulator should resemble the following figure.
Click the copy icon. 
Your computer's clipboard now contains the step test data.
Start PID Loop Analyzer. Select Enter Data then CSV Data. Paste (Ctrl V) the step test data into the dialog box. Select FOPDT (non-integrating) and enter the data as shown below.
Click OK. PID Loop Analyzer will display your original process data and newly developed process model in the left trend box. The green trace is the original PV data; the white trace is the controller output, and the yellow trace is the process model. You can adjust the model by manipulating the model parameters located underneath the trend box.
The right side displays the calculated PID parameters and the loop's response to a five percent set point change. Note that I set Lambda to three times the process open loop time constant.
Switch back to PID Loop Simulator (hopefully you left it running) and input the calculated tuning parameters. Perform a series of closed loop step tests. (Step the set point with the controller in automatic.) Verify it responds as expected: The process variable should reach the set point in four times lambdas, one minute in this case.
Please note an inconsistency: you define Process Gain as Percent Span per Percent Output in PID Loop Simulator, but PID Loop Analyzer displays it in Engineering Units per Percent Output.
I left many details out of this brief example. I am developing a comprehensive lesson and will publish it here on my website when I finish, or perhaps I will contentiously update this document instead. In the meantime, please feel free to send me questions, corrections and recommendations.