PREFACE

Experimentation is fundamental to physiology.  Only by performing well-designed experiments have physiologists been able to get us to our present understanding of the integrated functioning of organelles, cells, tissues, organs and organ systems.  A goal of any physiology course is to introduce you to the experimental side of the subject.  By conducting experiments, you get an appreciation for how science ‘works’ and you gain better insights into the function of physiological systems. 

During this term, you will be performing a number of computer simulations designed to provide you with experience in the practical side of physiology:  designing and performing experiments, in this case of the virtual variety, and analysis and interpretation of the resulting data.  As you will see, the subjects covered by these simulations run the gamut from background material (e.g., enzyme kinetics and the physics of electricity), through some of the classic experiments in neurophysiology and muscle physiology, to replication of some very recent experiments that represent the ‘cutting edge’ of contemporary physiological research.

You will also learn that an experiment, even when carefully and specifically designed to answer a particular question, typically engenders far more questions than it answers.  Thus, in many simulations you will find links to other web sites where you can go for more information.  Where appropriate, a bibliography of published research or review articles is also provided to help direct you in your search for answers to your questions.

The computer simulations’ on which this ‘lab manual’ is based are organized as indicated in the flow chart to the right.  The Physiology Simulations Home Page provides links that will take you to the home page of the simulation with which you wish to work, either directly or indirectly via a Simulation Group Home Page.  On each simulation’s home page you will find links to the Simulation Overview page and the Protocols and Exercises page.  A third link (“Run the Simulation”) causes the simulation to load, ready for your use. In the Simulation Overview, you will find a brief introduction and presentation of what the simulation is intended to accomplish, followed by a picture of the simulation's display and a discussion of the display's appearance, features, and controls.  You will typically find a number of links to glossaries, explanatory essays, or even to other simulations, all intended to help you better understand the simulation you're working with at the time.  The Protocols and Exercises file, in addition to containing the experiments you'll be conducting using the simulation and questions to help you understand your data better, also includes a "Tips and Hints" section.  You will often find links to interesting web sites at the end of the Protocols and Exercises. In the Simulation Overview, you will find a brief introduction and

presentation of what the simulation is intended to accomplish, followed by a picture of the simulation’s display and a discussion of the display’s appearance, features, and controls.  You will typically find a number of links to glossaries, explanatory essays, or even to other simulations, all intended to help you better understand the simulation you’re working with at the time.  The Protocols and Exercises file, in addition to containing the experiments you’ll be conducting using the simulation and questions to help you understand your data better, also includes a “Tips and Hints” section.  You will often find links to interesting web sites at the end of the Protocols and Exercises.

You’ll probably want to print out the “Simulation Overview” and the “Protocols & Exercises” prior to working with each simulation.  I would recommend that you read through those documents before you actually run the simulation. 

The simulations have been tested for compatibility with Netscape Navigator and Communicator (v. 4.5 or later) and Microsoft’s Internet Explorer (v. 4.0 or later).  They may not run properly with earlier versions.  They have not been tested for compatibility with other Internet browsers such as ICab, Opera, Amaya, or NeoPlanet.  They may run properly using those browsers, but they may not.  If you encounter problems running the simulations with other browsers, you may need to download the latest version of the browser provided by Netscape or Microsoft.

Once you are through reading this Preface and feel comfortable with the information it contains, click the “Back” or “Return” button at the top of your Internet browser.  This will return you to the Physiology Simulations Home Page from which you can follow links to the simulation you wish to run.

Bug reports, errors, suggestions for improvement, etc. should be sent to me using the e-mail link on the simulations’ home pages.

INTRODUCTION

Since you’ll be accessing and running the simulations using an Internet browser (e.g., Netscape Navigator™ or Microsoft Internet Explorer™), I’ll assume you already have a browser installed on your computer and have learned how to use it to access web pages.  If not, you’ll need to do this before proceeding.

Let’s discuss how you actually go about running a simulation and using its features to perform virtual experiments..  This will entail some fairly detailed discussion about the features common to the displays provided by programs running in a windows-based environment such as Microsoft’s Windows, MacIntosh’s OS, Linux, or Unix.  First, though, we’ll start by refreshing your memory about how to use the mouse to work with programs running in a windows-based operating system. 

Working With The Mouse

When you are instructed to click on some feature of a simulation’s display, that means to use your mouse to position the cursor (pointer) over the feature and then click the left mouse button one time.  “Double-clicking” means do the same, except click the left mouse button two times in rapid succession.  The term “click-&-drag”, or simply “drag”, means to place the cursor over some feature of the display, such as when a moving a slider or highlighting a group of cells in a spreadsheet, click the left mouse button and while keeping pressure on the left mouse button, move (drag) the cursor to the desired location.  Once you’ve reached the desired location, release the left mouse button.

Preparing To Run A Simulation

Before proceeding with any simulation, you should carefully study its “Simulation Overview” and “Protocols and Exercises” files.  You should also print any data sheets that are supplied in the Protocols and Exercises file and have those close at hand.  This will ensure you’re ready to get the most out of the time and energy you spend working with the simulation. 

Depending on which particular simulation you’re planning to work with, you may need a ruler for measuring certain features of the simulation’s output such as the amplitude (height) of a graph, the width of a peak (such as an action potential), or the length of a scale that you’ll use to convert your data into units such as grams, newtons, or millivolts.

In some cases, one simulation may require data from a simulation you’ve run previously.  If so, be sure to have those results available. 

Starting A Simulation

Once you’ve accessed a simulation’s home page and are ready to work with the simulation, load it by clicking the “Run the Simulation” link.  After a short delay, the simulation’s display will come up on the screen (see “What Do The Simulations Display?”, below).  You should see an “Applet xxx loaded” or “Applet xxx running” (where “xxx” is the filename for the simulation you’re working with) in your browser’s status window.  You are now ready to start working through the simulation’s exercises.

Important:  if a simulation fails to load once you’ve clicked the “Run the Simulation” link, or if it fails to work properly once it’s loaded, click on the appropriate “If the simulations won't run “ link (PC or MacIntosh) on the simulation’s home page.  That will take you to a listing of suggestions about possible solutions.   

What Do The Simulations Display?

Here's an typical example of the display you'll see when you're running the simulations:

This particular display is produced by the Voltage Clamp Experiment simulation.  The display for other simulations will differ somewhat, but this display contains all of the features you’ll be using, so we’ll use it to introduce you to the features with which you’ll be working.

Depending on the size of your computer’s monitor, the browser’s display may occupy so much of the viewing area that you can’t see the entire display of the simulation.  With Netscape Navigator or Microsoft Internet Explorer, you can close one or of the menu bars at the top of the screen and ‘free up’ some viewing area.  For instructions on how to do this, click here. 

When you first start a simulation, you will generally see a window that displays one, or perhaps more, blank x-y axes.  In this example, there are two sets, one for displaying I_m, the other for displaying dV_m.  (Don’t worry about what those variable names signify for now.  We’re just concerned with introducing you to the various features that you’ll encounter while working with the simulations.)  Depending on which particular simulation you happen to be working with at the time, you will be employing up to five types of controls, all of which are represented in this display:

1.  Sliders – similar in function to a scrollbar, sliders are used in conjunction with the mouse to make changes in the value of some parameter.  In these simulations a slider is usually functionally linked to a text field.

2.  Text fields – these are basically mini word processors that you can use with the keyboard to enter a numerical value for a parameter.

In this display, there are three slider/text field combinations, labeled [Na⁺], [K⁺], and d(V_m), located in the right side of the display. 

3.  Checkboxes – as its name implies you check one these little square boxes to provide the simulation with some information.  Checkboxes are provided with labels that indicate their function.  Checkboxes functions like a toggle switch:  clicking on an inactive checkbox ‘toggles’ it to the active state, and clicking on an active checkbox switches it to the inactive state.  There are three checkboxes , labeled Itotal, IK⁺, and INa⁺, located along the bottom edge of the display.  You can check – and therefore select or activate – as many checkboxes as are visible in the simulation’s display (two are checked in the above display).

4.  Radio buttons –radio buttons are little circles that function just like a checkbox, except that they are organized into sets and only one button in a set can be selected at a time.  In other words, they function like the station pre-set buttons on a car’s radio, hence their name.  Radio buttons are provided with labels, and also function as a toggle switch.  There are two radio buttons in the right-hand portion of the above display, labeled “dVm > 0” and “dVm < 0”, and the dVm > 0 is selected.  If you click on the dVm < 0 radio button, the dVm > 0 button will be ‘deselected’, and vice versa.   

5.  Buttons – three buttons (Go, Clear, Reset) are located at the lower right in the display. 

 All of these features (sliders, buttons, text fields, checkboxes, and radio buttons) will be used in various ways in the different simulations.  More complete descriptions of these controls and how to use them are provided below.

The Control Buttons

Running a Simulation (the Go button)

When you click the "Go" button, a simulation will be run using the parameter values that you have specified, and some sort of display – usually a graph of the results – will be generated. When the output is in the form of a graph, generally the graph for each subsequent run is displayed using a different line color.  In such cases, a legend indicating which color represents the 1st run, the 2nd run, and so on will be presented across the top of the display. This will make it easier for you to keep track of the effects of parameter changes you've made. Note, however, that after the 10th run, the line color reverts to black until you clear the display.

Other information may also be displayed along with the graph, depending on which simulation you are running.

Whenever you run a simulation, I strongly recommend that you use the data sheets provided in the simulation’s Protocols and Exercises section to record the parameter settings and the simulation results as you go. This will make it much easier for you to enter the data into a spreadsheet program for subsequent graphing and analysis

Clearing the Display (the Clear button)

Most of the simulations are written so that the results of each run remain on display. The intention of this feature is to allow you to readily compare the consequences of changes you have made in the simulation's parameters. However, after a few runs the display will probably become too cluttered to be useful. When you reach this point, simply click on the "Clear" button to clear the display, and you are ready to continue with more runs.  Note that clicking the "Clear" button does not reset the parameters to their original default values.  Instead, the values used for the last run are preserved.

Resetting the Parameter Values to Their Default Values (the Reset button)

Any time you wish to run a simulation based on the default values for the parameters, simply click on the "Reset" button. This returns the parameters to their original values and automatically runs a simulation based on those values.  Usually, the Reset button does not clear the display, but before you click the Reset button, be certain to record any data you don’t want to lose.

Changing the values of a simulation's parameters

There are three ways to change the value for the parameters used in a particular simulation.  The method of choice depends on your individual preference and on the magnitude of the change you wish to make.

1.  Using the Sliders

There are three slider techniques you can use to change a parameter's value:

• click-&-drag the slider to the desired value (displayed in the text field above the slider).

• place the tip of the mouse cursor in the 'track' of the slider and click the left mouse button. This will change the value of the slider by a number of units (usually 10) every time you click the left mouse button. To increase the slider's value, place the tip of the mouse cursor above the slider; to decrease it, place the cursor below the slider.
• click the 'up arrow' or 'down arrow' at the ends of the slider's track. Each mouse click will change the slider's value by one unit.

Important! You may encounter a particularly aggravating problem when using the sliders to change parameter values.  Specifically, the slider may lock into the ‘on’ mode and become unstable, refusing to stay at the value you’ve moved it to with the mouse cursor.  Typically when this happens, the appearance of the slider changes in unpredictable, often bizarre, ways.  The problem apparently stems from the implementation of the JAVA programming language by your browser.  Windows™ and OS™ versions of browsers seem particularly vulnerable to this bug, while Linux versions seem relatively immune. You can usually avoid the problem by not moving the slider too rapidly when employing technique #2 or #3 above.  In other words, only use #2 or #3 if you’re going to make a single discreet change in the slider’s setting (by a single mouse click).  Making large changes in a slider’s value by holding the left mouse button down with the cursor placed in the slider’s track (or on the up/down arrows) is very apt to cause problems.  Instead, either ‘click-&-drag’ the slider to its new position, or use the text field to change the slider’s value (see below). If the slider does start to function incorrectly, you have a few options.  Try clicking the Clear or Reset button; this will often restore the slider’s normal behavior.  If not, you can still use the text fields to change parameter values, but be careful to keep the cursor well away from the problematic slider.  In extreme cases, you may have to exit the simulation and start over.  Be sure to record any data you need before you exit the simulation.

That one problem aside, you will probably find that the sliders are the easiest way to change a parameter's value, particularly if you are making large changes and don't need the slider set to a particular value.

2.  Using The Text Field 

You may prefer to change the parameter's value by using the text field immediately above the slider. Simply double click anywhere in the text field to highlight the number and type in the desired number. Whatever you type will overwrite the current entry.  The corresponding slider’s position will change to match the numerical value you type in its text field.