Goals

(1) You should become versatile with the use of the electrophysiological computer accessories
(2) You will achieve the above in the context of learning about physiology literature.

A few tips on using your Macintosh

Most people primarily use a "WinTel" (Intel chip running Microsoft Windows), sometimes called a PC ("personal computer" somehow came to mean this type of computer, originally an IBM work-alike). That is why I thought this mini-tutorial might be useful, since the PowerLabs are based on the Macintosh G4 towers using Mac OS 9.x.

Make a folder for anything you want to save

It is very useful to be organized (i.e. to be a good file clerk). Folder (Mac) = Directory (PC). Double click on the hard drive and you will find a folder I made called Physiology. Double click Physiology. Pull down under File to New to Folder. Click on the title (Untitled folder) and delete this name and name your own folder. Remember how to find your way to your folder for saving.

Launching programs

Pulling down under the Apple logo (upper left), we get the Apple menu items. I've added aliases to some programs we will use under the Apple menu. I have these programs at the top of that list by putting an exclamation point (!) to get them ahead of the rest of the alphabetized items.

Toggling from program to program

The upper right will show the program you are using, and pulling down from the upper right will let you switch to another program that is already open.

"Minimizing" an application

Sometimes your application fills the screen and you want to see something on the desktop behind the application that is running. Pulling down under the upper right gives you the chance to hide your application. This is familiar to PC aficionados (and Mac OSX) as clicking to minimize. The program jumps back to the foreground just by pulling down from the upper right to that program (the logo is lighter when it is hidden).

Why Mac in a PC world?

(1) Before Windows 95, PCs were really user unfriendly, while Macs from the mid 1980's were intuitive.
(2) Mac also stayed alive in a David (Mac) vs. Goliath (PC) world by targeting schools, so many people knew how to use a Mac.
(3) In general, a Mac could always do anything a PC could do, but there was a time when many things, especially imaging, and, for you folks, physiology, could only be done on Macs.

That is why, even though SLU reflects the general population (PC > Mac), the Science and Math departments still have a lot of Macs.

How best to save your work to home

These Macs have a zip drive (I think 100 MB). While they make Mac formatted Zips, it is important to know that Macs can read PC formatted Zips. (The reverse is rarely the case.) So I always use a PC Zip so I can carry stuff from the Mac to the PC or the PC to the Mac.

Tutorial on writing a paper with a reference data base

Biologists writing papers and grants not only use word processors, they use reference data bases. Consider the differences in how citations appear [a] in the paper and [b] in the references. Examples:
(1) J. Biol. Chem., [a] (author, date), [b] numbered, alphabetized, most information but not title.
(2) The FASEB J., [a] (number), [b] numbered, but in order of appearance, all information.
Also, there are many variations on style, like whether the date is in parentheses and whether the volume is bold.

Suppose that for 5-10 years, a PI (principal investigator) is working in a sufficiently restricted area that (s)he cites many of the same papers in the references of many papers or grants. Suppose also that these are submitted to several journals and agencies. Or even considder, perish the thought, that J. Biol. Chem. rejects your paper but you want to try to publish it in the FASEB Journal. You could spend a lot of time re-typing the references in a different specific format. In order to avoid this tedious chore, references are typed one time and maintained in a reference data base where the program (here we will demonstrate Endnote) can be used to set the style for a particular journal. It is also possible these days (though we will not demonstrate it this time) to obtain the reference from the National Library of Medicine (and thus not to have to type it into your data base at all). If the style of a particular journal of interest is not in the menu, you can make your own.

Using system 9 on the old G4's I've set up a small exercize. Pull down under the Apple (upper left) to launch !Endnote. You will be asked which data base to open (and where it is). On the Macintosh hard drive is a folder called Physiology, and, in there, is a folder called Dr. Stark, and in there is a file called "New Endnote ref 95." Open that, and you'll see the many papers I've been citing in papers I've been writing. Double click one and you will see how all the information is entered.

As a reminder, you can switch from program to program on the Mac by just clicking on the document you are using (if you can see it) or pulling down under the upper right to select the program you want to toggle to. Pull down under the Apple to launch WordPerfect. Write a little text. In the old days, people always typed The phrase "The quick brown fox jumps over the lazy dog" to test typewriters because it used all the letters in the alphabet. Go to EndNote. Click on a reference. Pull down under edit and copy. Click over to Word Perfect and pick a place you want to pretend this reference is relevant and go under edit for paste. Note that all that shows up is author, year, and a #number identifying the data base entry, all in brackets. The brackets signal the program that that is a reference. Do this several times with several different references Save it (give it a name and select where you are saving it). Go to Endnote. Pull down under styles, and you will see some styles I've written and used. Pick one. Under paper, pull down to scan and get a window. The number 1 is good, 0 means you have used brackets for something other than a reference which is no real problem, 2 or more means that Endnote cannot determine which reference you mean (and that is a problem). If you did what I told you, you will have only 1's. Pull down under paper to format and it will default to save a WordPerfect file with your name followed by the journal you selected (note where it is saved). Now click to WordPerfect and open this new paper and note that the references are added at the end and, in the text, the citations are made in a way that is used for that journal.

Working with the computer interface

Preliminaries:


[Everything will probably already be on correctly.]

(1) The amplifiers have no on-off switch, so we handle that by plugging them in.
(2) These PowerLabs were purchased when input of such an interface into the computer was via SCSI, and the general rule is that the SCSI device should be on before the computer (not
hot-swapable like USB).
(3) After the PowerLab is on, turn on the computer with the tower or the keyboard button.

Recording with the force transducer

(1) Launch Chart. Note that there are 8 channels, the bottom 4 of which are bogus since there are only 4 inputs, and the bottom 4 are turned off.
(2) Turn off 2, 3, and 4 and pull down the bottom lines to the bottom to fill the screen with channel 1.
(3) Feed the force transducer into the bridge amplifier (x1 gain will work), and feed that into the PowerLab (gain of 100 will be sensitive enough).
[gain is second up-down arrow toward upper right]
(4) Start
(5) Note that the trace might be off scale - and here the position on the bridge helps a lot. It's a 10 turn pot (potentiometer = variable resistor).
(6) Get the trace centered and try the force transducer with some little finger twitches.
(7) Change the gain and notice the difference in size of recorded finger twitches. [understanding gain is fundamental]

We can calibrate the force transducer

(1) Note that the ordinate is in mV (which definitely does not reflect force).
(2) Start the record (on screen), put on a 5 g (or 10 g) weight, note the deflection (about 10 mV [or 20 mV])
(3) Understanding gain is fundamental, as stated above. What happens to the deflection for the weight when the gain is switched one step up or one step down?
(4) stop the record.
(5) Set the cursor [carefully!] on the low and high and note that you can see the readings (toward upper right)
(6) Pull down under units of conversion, on two point conversion, set your low and high readings on the left and 0 and 5 (or 10) on the right [then select g].
(7) Click OK and note that the ordinate is now in g.
(8) Maybe some groups have an upward deflection when the weight is put on. Why? How can you change this?


For the purist, force, is actually change in momentum per unit of time. In the cgs system, force is grams times cm divided by seconds squared, called dynes which is 10 to the -5 newtons (the mks unit). This, despite the transducer is called a force transducer and the one graph in your text (Silverthorn 3 ed) that has units for tension, Fig. 12-19 has units of kg.

Processing the data on Chart and on the cumputer

I. You can write comments


(1) Click on a part of the record and note the vertical line
(2) Pull down under command to add comment (alternatively the Apple key on the left or right f the space bar and K)
(3) Type your comment and OK that
(4) a click on the numbered comment will show it to you

II. You can copy and paste (a mini-PhotoShop tutorial)

(1) Under Aple menu items, launch PhotoShop
(2) Select a small portion of your Chart record with the Shift key and the mouse
(3) Go up to the magnifying glass to get a zoom
(4) Under Edit, copy the zoom
(5) Toggle to Photoshop and ask for a new document
(6) It asks you what size and suggests dimensions - these are the size of what you copied (!) so Just say OK
(7) Paste

Photoshop is a very useful program (but I won't show you more than this for now).
(1) You can add labels like I did on this picture I present for your cardio lab
(2) You can make complex "plates" like this one I did for my research


This page was last updated 8/24/05

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