Neuron Simulator App

Graph Settings

The graph settings control which parts of the graphs are visible, the limits of the graphs, and some other features you see on the page. The checkboxes control which traces are displayed, and the toggle switches control whether certain graphs are displayed. The channel gates will be of interest to those familiar with neuronal modeling, and details can be found in the published model. Here, we’ll just explain that the variables m and h affect the sodium current, n affects a fast potassium current, and s affects a slow potassium current. A user may wish to disable certain traces in order to simplify the graph and focus on certain features of interest. For example, one might be interested in only observing the membrane potential. Likewise, we can hide the channel gates graph completely using the toggle switch. Note that hiding a graph reruns the entire simulation, and the remaining graph will become larger.

Below the controls for the channel gate graph are controls for the membrane currents graph. The checkboxes control the visibility of the three membrane currents that are referred to using “I” as the general variable for current. These variables are: sodium (labeled INa), fast potassium (labeled IKf), and slow potassium (labeled IKs). The membrane voltage (Vm) is superimposed in this graph as it was in the channel gate graph. For demonstration purposes, I will uncheck the boxes for the currents and observe only the membrane voltage.

Below the checkboxes are several text boxes that control the limits of the graphs. The setting labeled “Run Length” controls the total time of the simulation, in milliseconds, which appears on the x-axis in the graphs. The settings labeled “Channel Gates Range”, “Voltage Range”, and “Current Range” control the vertical limits for the respective traces. Each setting includes a minimum and a maximum value, allowing the user to focus on any section of the traces that is desired.

There are two more controls in the graph settings area to notice. The slider labeled “Animation Speed” controls the speed at which the traces appear on the graph from left to right. Higher values will result in faster animations. Note that this does not affect the overall speed of the simulation. The final part of the graph settings is a button labeled “Show/Hide Parameters”. Clicking this button toggles the view of all model parameters. This feature is only recommended for advanced users who are familiar with neuronal modeling methods.