When you start the problem you are given a cage of a population of creatures collected in the field. Each of these creatures will display one of two to six different traits of one to three particular characters (for example, if the character is Body Color, the traits might be Red Body and Green Body). Your task is to discover how these characters are inherited. You determine this by crossing particular individuals and observing their offspring. You then use the resulting data to deduce the underlying genetic models that determines the inheritance of these characters. You must decide when you have collected enough information to be convinced that you are right - the program will not tell you the right answer (except when in Practice Mode).
When you start a new problem, VGLII randomly chooses one to three characters from a list of possible characters. It then randomly chooses genetic models from a list of possible genetic models. The range of possible models is be custom-configured by your instructor when she creates a problem type; different problem types can have greater or fewer possible models and Practice Mode can be enabled or disabled for a particular problem type. Since this assignment is random, the same character can be inherited in different ways in different problems.
Next, VGLII chooses particular traits of each character and assigns them randomly to particular genotypes. A population of individuals with random genotypes is then generated; these individuals are placed in Cage 1.
Your task is to cross individuals from different cages and observe the resulting offspring. From these data, you will determine the genetic models of how your particular characters are inherited.
All the problems in VGLII involve genetic models with genes that have either two
or three alleles. Based on
this, there are several features that can vary:
To run VGLII simply double-click on the VGLIIx.x file. Note: Be sure to have the Problems folder in the same folder as the VGLIIx.x file. The toolbar buttons are shown below:
When you start VGLII, you will see a toolbar like this:
From the "File" menu, select "New Problem" or simply click on the "New Problem" button on the toolbar and you will see a list of problem type files. The files are listed in increasing order of difficulty. Additional problem type files can be generated using the VGLAdmin program. Select the file and click on the "Open" button.
Once you start a problem, a window (Cage 1) will be opened up on the screen. This cage is the starting point for your project. The organisms can be, but are not necessarily, pure-breeding.
Cross 1: Parents: Five/Red male from Cage 1 X Five/Blue female from Cage 1 Offspring: 11 Five/Blue (in Cage 2) 16 Five/Red
In practice mode, a cage will look like this:
This is the same as in Regular Mode, except that the model and genotypes can be seen.
You can use this feature to load up previously saved problems that you might have been
working on. To open a problem you can either select "Open Problem" from the drop-down
"File" menu or simply click on the "Open Problem" button on the toolbar. A dialog box
will open up to assist you in selecting a file. Browse to the directory in which the
problem file is stored. Select the file and click on the "Open" button. VGLII will read
the file and will open up the problem and bring it in the state* you last left it in
before you saved and closed the problem.
*state - state in this context is defined as the entire collection of cages created by the user, including cages that were created by the user but were kept closed during the course of problem work. Simply stated, this means that when you open a problem, VGLII will display all the cages created by you up until the point you closed the problem.
You can use this feature to save your current work to a file. To save your work you can either select "Save" from the drop-down "File" menu or simply click on the "Save" button on the toolbar. A dialog box will open up to assist you in saving your work to a file in the directory of your choice. Browse to the directory in which you want to save your work. in the "File Name" field enter the name of the file you want you want to save your work as. Then click on the "Open" button. This will create and open a file with the name as specified in the field and will store your current work in it. The file will have a .wrk extension.
This is the same as "Save a Problem" except that it creates a copy of the file you have already created but with a different name.
You can use this feature to close a problem that you have been working on. To close the problem that you have been working on select "Close Problem" from the "File" menu or simply click the Close button on the toolbar. A dialog box will pop-up to confirm your decision to close the problem. If you select "Yes" and if you have any unsaved work then the application will prompt you to save your work. If you select "Yes" then a dialog box will pop-up to assist you in saving your work to a file in the directory of your choice. If you select "No" the application will close the problem without saving any of your work.
To cross two organisms you first need to select a male organism and a female organism from any of the open cages (the male organism and the female organism can be from different cages). To cross these to organisms and create the set of offsprings that they would produce, select "Cross Two" from the "Utilities" menu or click on the "Cross" button on the toolbar. This will create a new cage containing the set of offsprings of the two parents used in the cross.
Super cross allows you to simulate many replicates of a particular cross. This can allow you to get a large number offspring for statistical analyses. Select two organisms for crossing and then choose "Super Cross" from the "Utilities" menu. You will be asked to select the number of offspring for the Super Cross. Please note that, in the real world, this would be very expensive and time-consuming; you should use it sparingly.
To print the field population (Cage 1) and all the cages you have generated so far, either click the Print button (shown at left), or select "Print Work" from the "File" menu. You may need to set up the printer first; you do this by selecting "Page Setup" from the "File" menu.
You can use this feature to store your work into a file in printer friendly format; this file can be displayed in any web-browser and many word processors. To print to a file select "Print To File" from the "File" menu or click on the "Print to File" button on the toolbar. This will open up a Dialog window to allow you to give the file a name and destination of your choice. Once you have given the file a name and decided on the location click on the "Print" button. Your work will be saved in a printer friendly format into a file. The file will have a .html extension.
By selecting one or more Cages and choosing "Create Summary Chart" from the Utilities menu, you can have VGLII count the number of each type of organism found in the selected set of Cages.
First, double-click on each of the cages to select them for summarization; their inner border will turn red to show that they are selected. You can unselect selected cages by double-clicking on them; you can unselect all cages by choosing "Unselect All" from the Utilities menu.
Once you have selected a set of Cages, choose "Create Summary Chart" from the Utilities menu and you
will see something like this:
You can choose which Characters to summarize by selecting the appropriate Characters at the top of the window.
The top line shows that this was a summary of cages 1, 2, 3, 4, & 5.
These were produced from crosses of two heterozygous parents; thus, we would expect a 3:1 ratio.
You can enter expected values into the cells in the Expected column. These must be whole numbers greater than zero.
When all the cells have valid values in them, VGLII will display the χ2 value and the corresponding p value.
In this case, the observed ratio is 103:42 which appears very close to the expected 3:1.
This is confirmed by a p-value greater than 0.05. Thus, these data do not deviate significantly from a 3:1 ratio.
You can use this feature to close/re-open any of the cages you have created till now. Select "Cages" from the "Utilities" menu. A window will pop-up with the list of all the cages you have created till now. The ones which are currently visible will be checked on the rest will be check-off. Click on the "Visibility" option beside each Cage listing to make that Cage visible/invisible.
You can use this feature to re-arrange the cages you have created in an orderly fashion. Select "Re-arrange Cages" from the "Utilities" menu. All the cages that are currently visible will be lined up one below the other and left to right.
To get more details and a detailed diagram about the phenotype of organisms in a cage, you can click on the image of the phenotype shown in the cage. This will pop-up a bigger and more detailed image of the organism highlighting the phenotype in question. Note that these images are rather primitive; they are only designed to illustrate what the combined phenotype might look like. One is shown below:
The Model Builder is accessed from the "Utilities" menu. It allows you to specify the details of the genetic model in your problem. You begin by specifying general features of the model; these then lead to more details. You can also specify some crosses that give information relevant to your model. Your instructor may require you to fill in the Model Builder for grading your work.
To get more details about the VGLII application you can select "About VGLII" from the "Help" menu or simply click on the "About VGL" button. This will pop-up an information window.