SQUID An Introductory Tutorial for GENESIS, XODUS, and the HODGKIN-HUXLEY model By M. Nelson, Caltech, April 1989 - Modified by D. Beeman, June 1991, Dec 1994 - Modified by E. Vigmond, September 1993 Installment 1 - The Basics As an introduction to the general neural simulation system (GENESIS) and the x-based online display utility for simulations (XODUS), we have put together a demonstration simulation and tutorial (SQUID) which will help you learn how to use these tools for constructing your own simulations and for customizing your user interface. In the process of working through this tutorial, you will also learn something about the Hodgkin-Huxley model. This program may serve as a good starting point for those of you who plan to work on single-cell models for a course project. The Model ========= For the time being, we are going to simulate a single axon compartment with active Na and K conductances, as described by Hodgkin and Huxley for the squid giant axon. In other tutorials we will link compartments together to form a simple model of an entire neuron with a soma and dendrites (the Neuron tutorial), model a cable with many compartments (the cable tutorial), and build neural circuits with connected neurons (MultiCell and tritonia). For now, we confine ourselves to a single axon compartment. Running the Simulation ====================== The model has already been initialized with some reasonable parameter values, so all you have to do to run the simulation is: click on the ``RUN'' button in the ``Simulation Control'' panel The simulation which you just observed was for a constant current pulse, which is shown in the lower left graph panel. The upper left graph shows the membrane potential. You can see that 3 action potentials were generated during this 50 msec simulation. Now let's change the injection current and see what happens. At the bottom of the screen is a control panel labeled `Current Clamp Mode'' and below it is a panel with five dialog-buttons. They have both the properties of a dialog box, which accepts input from the keyboard, and a button that executes a command script when it is pressed. In order to change the injection current: position the cursor to the right of the last digit in the "Pulse 1 Current" field and click in the dialog box with the left mouse button You should see the little ``^'' symbol move to the new cursor location. Let's change the peak injection current from 0.1 to 1.0. type to backspace over the 0.1 and then type 1.0 The value in the dialog field should now be 1.0. At this point we need to activate the dialog button to send this new value to the simulator. There are two ways to do this; you can either hit when the mouse is within the dialog field or you can click on the button with the left left-mouse button. We will now try both techniques. First, make sure the cursor is somewhere in the "Pulse 1 Current" field (it will be a vertical bar, not an X), and then hit anywhere in the dialog field If this successfully actived the button, you should see a message appear in the GENESIS command window. The message should say something like "Setting /pulsegen level1 1". You also could have activated the dialog-button by clicking on the box at the left. Do this now: click on the "Pulse 1 Current" button at the left of the dialog area again you should see a message appear in the command window. Note that you normally only have to do one of these two things to activate the button. The important point, however, is to make sure that you always do at least one of them, either hit or click on the button. Otherwise the simulator will not know about the changes you make to the dialog. Now we'll run the simulation again. click the "RESET" button on the control form click the "RUN" button on the control form There should be a dramatic change in the time-course of the membrane potential at this higher current injection level. Experiment with the injection level to see what happens to the axon at higher injection currents. Also try decreasing the injection level until an action potential is no longer elicited by the stimulus. What is the threshold for producing an action potential in this compartment? You may also experiment with trains of short pulses. Set the "Pulse 1 Width" dialog field to 1 msec and click on the "Single Pulse" toggle so that it reads "Pulse Train". Now vary "Onset Delay 1". What is the minimum interval between action potentials that you can achieve? Voltage Clamping ================ You can also perform voltage clamp experiments in this simulation. click on the "Toggle Vclamp/Iclamp Mode" button at the bottom of the control form. You should notice several things changing on the screen. All the changes are being controlled by the script attached to the "Toggle" button. The integration time step has been reduced from 0.1 msec to 0.01 msec, and a new "Voltage Clamp " form has appeared in place of the "Current Clamp" form. Again, reasonable default values have been selected , so all you have to do to run the voltage clamp simulation is: click the "RESET" button on the control form click the "RUN" button on the control form Changing Extracellular Concentrations ===================================== You can alter the extracellular concentrations of the ions through the "External Concentration" form". Any changes in concentration will cause the reversal potentials to be recalculated. To reset the values back to the initial ones, just click on the "Default Values" button. Controlling Graphs ================== The graph of the clamp current (lower left panel) has gone off scale. In order to rescale the graph: click on the "scale" button in the upper left corner of the graph A form containing dialog buttons for the coordinate range should appear. Adjust ymin and ymax to bring the graph into range. Remember to activate the dialog buttons by either hitting in the dialog field or by clicking on the button after you've made your changes. The x-axes of all graphs are automatically scaled to the time of the simulation. click on the "DONE" button to hide the "Graph Scale" form It is often convenient to leave the "Graph Scale" form visible if you are going to be making alot of scale changes. Just drag the form to a convenient place on the screen and leave it there. The "Graph Scale" form also has an "overlay" dialog button. When overlay = 1, any existing plots in the graph will be held and new simulation results will be overlayed. Try this now. Set overlay = 1 for the graph of membrane voltage and run the simulation at several values of the clamp voltage (remember to RESET between runs). To clear all the graphs, click on the "Clear Graphs" button. This will not RESET the graphs; you must do that yourself. State Plots =========== One can learn a great deal by studying plots in which one of the Hodgkin-Huxley channel activation parameters (the K activation "n", the Na activation "m", or the Na inactivation "h") is plotted as a function of the membrane potential, V. (See, for example, Chapter 5 of "Methods in Neuronal Modeling", by Koch and Segev.) In order to view such a plot, click the left mouse button on the "toggle" button labeled "State Plot Hidden". The label will change to "State Plot Visible", and a state plot graph will appear. Clicking the button again will hide the graph. The default plot is to show the K channel "n" parameter on the y-axis and the membrane potential on the x-axis. The dialog boxes at the bottom of the graph allow you to change these defaults. Channel Blocking ================ In order to explore the effects of blocking one of the channels, you may click on one of the toggle buttons for blocking and unblocking a channel. When a channel is blocked, its conductance is set to zero. Activation parameters for a blocked channel are still calculated and may be plotted, but are relatively meaningless because they will have no effect on the membrane potential. Printing Graphs =============== You can get a printout of a graph by positioning your cursor withing the graph area and typing . (You should check with your system administrator to be sure that your workstation has been set up to print the postscript output produced by this command.) An even better way to capture a portion of the screen is to use a screen-grabbing utility like "xv" or "xgrabscr" from your favorite X-windows archive site. Units used in the simulation ============================ Units: time msec length um (microns) potential mV conductance mS (mmho) resistance kohm capacitance uF specific axial resistance kohm-cm specific membrane conductance mS/cm^2 specific membrance capacitance uF/cm^2 ------------------------------------------------------------------------------