DATA ANALYSIS WITH THE MACINTOSH COMPUTER AND CRICKET GRAPH

 

The use of computers in the biological sciences is becoming increasingly widespread at a rather remarkable rate.  Personal computers are used for data acquisition, data analysis, preparation of illustrations and writing of scientific papers.  In this high-tech age it is imperative that all biology students, no matter what their specific interest is, have some experience in the use of personal computers. 

 

In Cell Biology laboratory, you will be gathering data nearly every week.  Part of your job is to graph these data and interpret them.  In the past this has been a tedious exercise because all graphs were made by hand, and in some labs this required many dots plotted on graph paper and much time.  With the Macintosh computers and Cricket Graph your job will be simplified and graph preparation time shortened considerably because you can easily print a copy of your graph.  Therefore, you will spend more time thinking about and interpreting data. 

 

The objective of this exercise is several fold.  First, you will learn how to use the Macintosh computer employing a program called Macintosh Basics.  Second, you will learn how to enter data into Cricket Graph and how to make several types of graphs in this exceptionally easy to use graphing program.  Third, we will discuss the role of hypotheses formulation in the scientific method and why hypotheses are crucial to the interpretation of data obtained from experiments.  A major aspect of data interpretation is whether the data are good: That is, what do you look for in your data to determine whether the data are good?  Fourth, you will learn how to use the Pipetman properly.

 

The Lab Exercises

I.  Slope and Equation of a Line

In lab you will often be asked to determine the slope of a line of a graph.  In doing this, Cricket Graph will present you with the equation of a straight line.  Hence, you must know what the slope means and where you get this from the equation of a straight line.  Study the graph below to see how the slope of a line is determined.

The slope of the line is called m where

 

m = ∆Y/∆X.

 

Thus, m is a ratio: the change in Y divided by the change in X.  The equation of a straight line is given by

 

Y = mX + b

 

where b is the Y axis intercept.  With this equation we can determine Y if we know m, X, and b.

 

Problem:  First, explain why the product of mX can be added to b, the Y intercept.  Second, why must the product of mX be added to b?

 

II.  Macintosh Basics

 

The Macintosh Basics program was designed to introduce first-time Macintosh users to the Macintosh platform.  To open the program, double click on the Macintosh Basics folder in the hard-drive window and then double click the Macintosh Basics icon (little dark-haired guy smiling).  First work through the mouse skills tutorial (pointing, clicking and dragging) and then perform all seven tutorials in the Main Topics menu.  This should take 25-30 minutes.  If it takes longer do not worry.

 

III.  Cricket Graph: Creating a New Data Window

 

New data windows appear as Data #1, Data #2 and so on.  The number of data windows you may have open at one time is limited only by the amount of memory allocated to Graph III.

There are two ways to create a new, untitled data window:

 

1.  Start the Graph III application from the desktop.

2.  If Graph III is already running, choose New from the File menu, then double-click the Data Window icon in the dialog box that appears (or select the icon and click OK).

Note: You can open a previously-saved data window by choosing the Open command from the File menu, then locating and double-clicking the name of the file you want to open.

 

Numeric and Alphanumeric Data

 

The first value you enter, paste, or import into a column in a data window determines the formatting of all other values in that column-as numeric or alphanumeric data.  For example, if you enter the word Quarter as the first value in a column, the column is formatted as alphanumeric data; if you enter 15 as the first value, the column is formatted as numeric (decimal) data.  If you enter an alphanumeric value in a column that is already formatted as numeric data, a dialog  box appears, asking if you want to change the format from numeric to alphanumeric (see below).

 

 

 

 

 

 

The Active Cell

The active cell in a data window is the one you are currently entering  data into; this cell always has a thick border around it. You can make any cell active by clicking it.

If the active cell is empty, a blinking data insertion bar appears both in the cell and in the formula bar at the tip of the data window.  If the active cell already contains a value, the entire cell is highlighted and its contents are displayed in the formula bar.

 

 

Moving Around a Data Window

 

Before you enter data, you should know how to move around a data window:

 

Use Return, Enter, down arrow or click in the cell

 

To move down one cell

 

Use Shift-Return or up arrow or click in the cell

 

To move up one cell

 

Tab or right arrow or click in the cell

 

T move right one cell (vice-versa to move left one cell)

 

 

 

 

 

 

Entering Data

 

To enter data in a data window:

 

1.  Open a data window.

 

2.  In column 1 type in Quarters; in column 2 type in Denis

 

3. Activate the first cell under Column 1 and enter 1st.

 

4.  Under Denis, enter 10

 

5.  Fill out the rest of the Quarters column and the Denis column with the data      illustrate in the figure below.  Press Return, Enter, Tab, or any arrow key, or click    another cell to accept the value and then move to the next cell.

 

6. If you make a mistake, use the Backspace key or Delete Key to remove incorrect          characters, then reenter the value.

Entering an Actual Data Set

Now let's practice by entering a real set of data obtained from the activity of an enzyme as a function of substrate concentration.

1.  First open a new data window.

2.  Then enter the data in the table below into the data window, being sure to        enter the appropriate information into column 1 and column 2.

[S] moles/L

Vo (moles/min)

1.0

1.17

1.5

1.50

2.0

1.75

2.5

1.94

3.0

2.10

3.5

2.23

4.0

2.33

4.5

2.42

5.0

2.50

 

3.  Create a graph by dragging across columns 1 and 2, or hold down the Shift key           and click each column.

 

4.  Choose Scatter from the New Graph submenu (Graph menu).  The scatter         graph is represented by an icon labeled Scatter.

 

5.  The New Scatter Graph dialog appears.  The columns you selected in the data             window are now selected in the dialog.

 

6.  Click OK.  The scatter graph appears in a new graph window. 

 

7.  Next "cleanup" the graph:

 

a.  In the Finder click on Options and open Show Graph Items

 

b.  Click on Plot Frame and Grids to remove this from the graph

 

c.  Click on Legend to remove the legend

 

d. Click on Graph Title to remove the graph title

 

8.  Turn the numbers on the x-axis 90 degrees by double clicking on an x-axis number, selecting 0 degrees and then clicking the OK button.

 

9.  Turn the y-axis label 90 degrees by double clicking on the label, selecting 0 degrees and then clicking the OK button.

 

10.  Decrease the axis division increments for both the x and the y axis by double clicking on one of the axes and do the following:

a.  Type in a new value for the increment.

b. Next, select the other axis and do the same and then click the OK button.

 

11.  Select ABC in the palette and type in a figure caption below the graph.

 

12.  Print

Curve Fitting

One of the advantages of Cricket Graph is that it fits best fit lines to data points in a graph.  This is a feature you will use repeatedly throughout the course.  To learn how to use the curve fitting routines, enter the following data set in a Cricket Graph data window.

Vo

[NZ]

1

10

2

20

3

30

4

40

5

50

 

1.  Highlight the data and choose Scatter from the New Graph submenu (Graph menu). 

 

2.  In the Finder, open Options and choose Curve Fit.

 

3.  In the submenu, select a curve fitting routine by clicking on the small black triangle in the Method box and select linear.  Click OK.

 

4.  Position the equation of the line on the graph where it does not cross the data points or the line fit to the data points.

 

Using On-Line Help in Cricket Graph

 

On-line help provides immediate information about using key tools, commands, and features without exiting Graph III.  To use on-line help:

1.  Press Commmand ?  The help window appears.  On the left side of the window is a list of topics.

2.  To view the information for a particular topic, click the topic's name.

 

IV.  Class discussion of hypotheses formulation and data interpretation (are the data good?).

 

V.  Discussion of the lab notebook (lab manual).

 

a.  Record date and experiment

 

b.  An objective or hypothesis should be written in the notebook for every experiment performed.

 

c.  The data should be recorded in the notebook .  If the data exist in a Cricket Graph data window, print the window and tape in the notebook.  Do the same with graphs made in Cricket Graph.

 

d.  Write a conclusion for each experiment. 

VI.  PROPER USE OF THE PIPETMAN

The automatic Pipetman will be used extensively in lab throughout the course to pipette solutions (Figure 3).  Because these pipettors are expensive (~$200.00 each), it is imperative that you learn to use them correctly.  The pipettes are adjustable to deliver different volumes of solution.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 3.  Parts of the Pipetman.  

The model you will employ is called the P-200 which delivers volumes from 1 to 200 µl (1 µl = 0.001 ml).  A stainless steel tip ejector is provided with all Pipetman models.  The recommended volume ranges for greatest precision are listed below:

 

P-200: 20 -200 µl;   P-1000: 200-1000 µl

 

DO NOT WIND THE P-200 ABOVE 200 µl AND THE P-1000 ABOVE 1000 µl!!

Operation of the Pipetman (Figure 3)

1.  Set the desired volume by holding the Pipetman body in one hand and turning the volume adjustment knob until the correct volume shows on the digital indicator. 

 

2.  Attach a disposable tip to the shaft of the pipette.

 

3.  Depress the plunger to the FIRST POSITIVE STOP.  This part of the stroke is the calibrated volume displayed on the digital micrometer.

 

4.  Holding the Pipetman vertically, immerse the disposable tip into the sample.

 

5.  Allow the pushbutton to return slowly to the UP position. 

 

6.  Withdraw the tip from the sample liquid.

 

7.  TO DISPENSE SAMPLE, place the tip end against the side wall of receiving vessel and depress the plunger slowly FIRST STOP, then depress the plunger to the SECOND STOP.

 

8.  After removing the Pipetman from the vessel, allow plunger to return to the TOP POSITION.

 

TEST YOUR SKILL WITH THE PIPETMAN (THIS EXERCISE IS TO BE PERFORMED BY EACH STUDENT)

 

Before you proceed with the other exercises in this lab, test your skill with the Pipetman.  With the P-200, deliver 200 µl distilled water (DW) into a preweighed weigh boat.  Reweigh the boat on the analytical balance and determine if you delivered accurately 200 µl DW.  Repeat the procedure but deliver 20 µl.