There are three main parts to the AP simulator interface: the graph display, the graph settings, and the stimulus settings. The graph display includes up to three graphs, some of which can be turned off if desired. One shows the membrane voltage with the channel gates. The second shows the membrane voltage again in comparison to membrane currents. And the third shows the stimulus that is applied to the membrane.
When you load the simulator page, it immediately begins a simulation with the default settings. The graph display appears at the top and shows how certain values change over time. By default, the display has a significant number of features that are visible, and it can be customized to hide features that are not of interest. The default layout includes three separate graphs: a top graph with several colored traces, a middle graph with more colored traces, and a third graph at the bottom with only a red trace. The top and middle graphs show what the model is doing, including values for the membrane voltage, channel gates, and membrane currents. The bottom graph shows the stimulus in red. This is the part of the simulation that you’ll be designing in order to make something happen in your virtual experiments.
Perhaps the most important value is the membrane voltage (Vm), which is shown in black. Other values available on the top graph are called Channel Gates, and they represent the level at which the various ion channels are open. Channel gate traces appear in additional colors, and they overlap with the trace for membrane voltage. The channel gates are physical mechanisms in the cell membrane. In the model, they have values ranging from 0 to 1, where 0 = fully closed and 1 = fully open. If you’re not familiar with the concept of modeling ion channels, a course or tutorial on computational neuroscience can help you get the most out of the simulator. See the references at the end for more information.
The middle graph is very similar to the top graph, and includes the membrane voltage. The difference is that the colored traces in the middle graph show membrane currents instead of channel gates. The channel gates directly control the membrane currents. The combined sum of the currents, shown in the middle graph, directly determine the overall membrane voltage. Observing the values of the distinct currents can be useful when studying their values relative to each other.
The final graph is at the bottom and shows the stimulus trace in red. Unlike the other graphs, this shows what you, the user, are actually doing to the membrane. We will see shortly how to set values for the current pulses to be injected. This graph shows the total current being injected at each moment in time during the simulation.