The basic unit for XPP is a file called an ode file that tells XPP the parameter and variable names and other named things. These files are editable ascii files. Use your favorite editor! For class, however, I will give you most of the files so you won't have to learn an editor. However, there will be occasions in which you will have to put in your own equations. It is then advisable to learn a bit about the input files.
The voltage clamp technique was used by Hodgkin and Huxley to determine the behavior of the ionic conductances responsible for the generation of the action potential. The basic circuit for the squid axon (whose owner is pictured above) is
Click here to load up the voltage clamp file and begin the tutorial. Several windows will pop up that we will look at later. The main window has a menu on the left and a graphics window in the middle. There are several parameter sliders and a thin window at the bottom that contains useful information. The top window is the command window and is often used for input. Three useful windows come up iconified: the parameter window, the initial conditions window, and the data viewer. Click on the parameter window to bring it up. Click in any of the windows to change parameters (don't do it now). Similarly, you can click in the initial conditions window to change initial data. The data viewer lets you look at the numbers that the simulation generates.
(If it doesnt appear, it could be that Netscape has stolen all the colors. To edit a previously defined curve, click (Graphic stuff) (Edit) and choose curve 1. Check to see that the INa is in the y-axis and change the color to some other number -- 0 will always work but is the same color as I. Then click (Ok))
Now click (Graphic stuff) (Add) and add IK to the picture with another color if you have the colors. Click (Ok) again. Now you will have three curves. The current is the sum of the early sodium current and the delayed rectifier potassium current. Note that negative currents correspond to flow into the cell and positive are currents exiting the cell. Notice that the sodium current is not monotone whereas the potassium current is monotone. The sodium first increases and then decreases. It decreases at a rate similar to the increase of the potassium current. The initial sodium current is very fast. To see what the conductances are doing, click on (Make window) (Create) to get another window. Next click on (Graphic stuff) (Remove all) to get rid of all but the main curve. Now click on (View axes) (2D) to get another dialog box. Fill it in as follows:
Hodgkin and Huxley repeated this experiment for many different voltage clamps. There are several ways to change the amount of the clamp. Click on (Parameter) and then type in Vclamp in the main window. Change it to 20. The type (Return) twice to exit the parameter changing. Alternatively, in the parameter window, edit the number next to Vclamp and click on (Ok) or better type (Tab) on the keyboard. Click on the main graph to make the current window the active window. Click on (Erase) in the main menu to clear the graph. Click (Initial conds) (Go) to run the simulation with a new clamp at 20 mV. Click on the conductance window and then in the main menu, click (Erase) (Restore). This erases the old graph and redraws with the result of the new simulation. Measure the maximum conductances and the time of maximum for the sodium conductance.
Change vhold from -60 mv to -80 mv. Re-integrate the equations. What are the maximal conductances? Explain how this is different from the previous values.
Click in the current window. Change vhold back to -60. Click on (Graphic stuff) (Remove all). Now click on (Initial conds) (Range). A dialog box will come up. Fill in the following entries:
NOTE XPP only saves the most recent result of a simulation so to get the results of several different simulations on the same plot in order to get hardcopy, you must "freeze" the graphs after each simulation. This is done by running the simulation, then clicking (Graphic stuff) (Freeze) (Freeze). A dialog box occurs. Just accept the defaults. Up to 10 curves can be frozen. They are named crva , crvb , etc. The (Graphic stuff) (Freeze) (Delete curve) lets you delete them one at a time and the (Graphic stuff) (Freeze) (Remove all) deletes all but the most recent curve.
Go through the book and look at some other manimulations you could do and try them. Click on (File) (Quit) (Yes) and then exit Netscape.