Frequently Asked Questions

Do I have to be connected to the web to use NIA?

Once NIA2 and XQuartz are installed, you no longer need an Internet connection. All content and simulation files are stored within the application bundle.

When I click the "Start the Simulation" button, what am I doing?

You are launching a set of panels and graphs using a special version of the NEURON simulator that is bundled within the NIA2 application. (On macOS, NEURON runs within XQuartz, so XQuartz will appear as the active application.) The launched simulation files are specific to the particular tutorial you have chosen.

NIA2 is running, but simulations are not working

Make sure to follow the installation instructions carefully. On macOS, ensure the latest version of XQuartz is installed and has been given permission to run in the background. Also make sure you restart your computer after installing XQuartz.

When I click Reset&Run there is no voltage change. What is wrong?

Unless you are in the Equilibrium Potentials tutorial, you probably forgot to insert a simulating electrode into your patch, axon or cell. Click the appropriate Stimulus Control button in the P&G Manager so as to open that panel. In the special case of the Equilibrium Potentials tutorial, you will only see lines at the values of ENa, EK, and the resting potential.

My simulation produces a trace that is uninterpretable—it certainly does not look like what the tutorial says I should expect. What is wrong?

You may have two or more Stimulus Control panels open by accident. Move one over and look underneath it.

My traces go off the plot. How can I replot them so they fit on the plot?

Put your cursor on the graph, click the right mouse button, and select View=plot from the submenu. The traces will be automatically scaled to fit the graph.

I have extra panels or graphs on the screen. What have I done wrong?

You may have double-clicked the buttons that bring up graphs or panels instead of single-clicking. Double-clicking will bring up the window twice. Alternatively, you may have multiple copies of NEURON running. This can happen if you fail to Quit a tutorial before launching another one. Make certain you Quit each tutorial before going to the next one.

I would like to move the labels to different positions on the graph. How do I do this?

With your cursor on the graph, click the right mouse button (or, on the Mac, the little box in the upper left corner of the graph) and select Move Text from the submenu. You can then grab the text with the cursor and move it.

Can I change the color or line width of the trace on a graph?

Yes. With your cursor on the graph, click the right mouse button (or, on the Mac, the little box in the upper left corner of the graph) and select Color Brush from the submenu. Select a color and line width in the pop-up menu by clicking its diamond and click the line to apply your selection. When you Quit the simulator for the tutorial, your changes will not be saved.

How does one right-click on a Mac one-button mouse?

Click the mouse while holding down the Control (ctrl) key.