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How close is close enough?

How close is close enough?. Part II Mendel vs 1000 Ideal Worlds. Build the world in BioBIKE biobike.csbc.vcu.edu.

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How close is close enough?

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  1. How close is close enough? Part IIMendel vs 1000 Ideal Worlds Build the world in BioBIKEbiobike.csbc.vcu.edu This demonstration is best viewed as a slide show,enabling you to simulate a session and make changes in cursor position more obvious.To do this, click Slide Show on the top tool bar, then View show.

  2. male-genotype female-genotype p p Pp Pp p Define an ideal genetic world How? - Define genotype

  3. Define an ideal genetic world How? - Define genotype - Define meiosis - Define gamete

  4. Define an ideal genetic world How? - Define genotype - Define meiosis - Define gamete - Define joining of gametes to form progeny

  5. Define an ideal genetic world How? - Define genotype - Define meiosis - Define gamete - Define joining of gametes to form progeny - Define how color is determined

  6. Define an ideal genetic world - Define genotype - Define meiosis - Define gamete - Define joining of gametes to form progeny - Define how color is determined - Define Mendel's experiment 929crosses

  7. Define an ideal genetic world - Define genotype - Define meiosis - Define gamete - Define joining of gametes to form progeny - Define how color is determined - Define Mendel's experiment Go to the BioBIKE Portalbiobike.csbc.vcu.edu

  8. Go to a public site

  9. Your name (no spaces) Enter a log in nameClick New Login

  10. Function palette Workspace The BioBIKE environment is divided into three areas as shown. You'll bring functions down from the function palette to the workspace, execute them, and note the results in the results window Results window

  11. HELP! PROBLEM Two very important buttons on the function palette: On-line help (general) Something went wrong? Tell us!

  12. Two very important buttons in the workspace: Undo (return to workspace before last action) Redo (Get back the workspace you undid)

  13. male-genotype female-genotype p p p What now? The first step in making the ideal world is to define what are male- and female-genotypes. Mouse over the DEFINITION button

  14. Click DEFINE to bring down the DEFINE function.

  15. A DEFINE function box is now in the workspace. Before continuing with the problem, let's consider what function boxes mean.

  16. Argument(object) Function-name Flag Keyword object General Syntax of BioBIKE The basic unit of BioBIKE is the function box. It consists of the name of a function, perhaps one or more required arguments, and optional keywords and flags. A function may be thought of as a black box: you feed it information, it produces a product.

  17. Argument(object) Function-name Flag Keyword object General Syntax of BioBIKE Function boxes contain the following elements: • Function-name (e.g. SEQUENCE-OF or LENGTH-OF) • Argument: Required, acted on by function • Keyword clause: Optional, more information • Flag: Optional, more (yes/no) information

  18. Argument(object) Function-name Flag Keyword object • Option icon: Brings up a menu of keywords and flags • Action icon: Brings up a menu enabling you to execute a function, copy and paste, information, get help, etc • Clear/Delete icon: Removes information you entered or removes box entirely General Syntax of BioBIKE … and icons to help you work with functions:

  19. Argument(object) Function-name Flag Keyword object • Option icon: Brings up a menu of keywords and flags • Action icon: Brings up a menu enabling you to execute a function, copy and paste, information, get help, etc • Clear/Delete icon: Removes information you entered or removes box entirely General Syntax of BioBIKE … and icons to help you work with functions: And now back to our show…

  20. The DEFINE function asks for two things: the name of the variable to be defined and the value it is to be given. Let's call the variable male-genotype. The value of male-genotype will be "Pp" Click on the variable argument box to open it up for entry…

  21. … and type male-genotype (remembering to connect the words with a hyphen), closing the box afterwards by pressing Tab.

  22. Tab closes the entry box and automatically opens the next one (if it exists). Type the genotype "Pp" (be sure to include the quotation marks) and press Enter.

  23. The definition is now complete. But it will not take effect until the function is executed Click the Action icon.

  24. … and click Execute.

  25. Notice that a new VARIABLES button appears. We'll use it later to access the newly defined variable. Notice also that the definition is confirmed by showing it in the Results Window

  26. Repeat what you did, this time defining female-genotype in the same way

  27. Now to define meiosis. Mouse over the DEFINITION button and click DEFINE, just as you did before.

  28. Click the name box…

  29. …type in meiosis, and press Enter.

  30. If you like, you can give a short summary in English what your function does, that is, what is meiosis. To do this, mouse over the summary icon…

  31. … click summary, and enter the summary of the function in the text box that appears. Finally, press Enter to accept the summary.

  32. How to define meiosis? It requires the diploid genotype of the organism and then chooses one of the chromosomes to go into a haploid gamete. The argument (input) to the function is the genotype. Click the argument box…

  33. … and enter the word genotype, a symbol that will represent whatever genotype the function is given. Then press Enter.

  34. What does meiosis do? You'll define this by putting the appropriate action into the form box. Click that box….

  35. …how to choose a chromosome at random? BioBIKE has a CHOOSE-FROM function that will serve our needs. Mouse over the ALL button…

  36. The ALL button provides BioBIKE functions in alphabetical order. Mouse over the C menu item…

  37. …and click CHOOSE-FROM.

  38. CHOOSE-FROM what? From the genotype! Click the sequence box…

  39. … and type genotype and press Enter.

  40. The definition of meiosis is now complete. To make it active, mouse over the Action Icon…

  41. …and click Execute.

  42. Notice that a new FUNCTIONS button appears. We'll use it in a moment to access the newly defined function. Notice also that the definition is confirmed by showing it in the Results Window

  43. Try out your new function. Mouse over the FUNCTION button and click Meiosis.

  44. Click on the genotype box of Meiosis. Provide it with male-genotype, by mousing over the VARIABLES button and clicking male-genotype.

  45. Execute your function as you do any other function, by mousing over the Action Icon…

  46. …and clicking Execute.

  47. The result of meiosis now appears in the Results Window. Execute the function a few more times to get a feel for what it does.

  48. With Meiosis in hand, you can now define the male and female gametes. Bring down a DEFINE box as you have previously and set the variable as male-gamete. (Be sure to remember the hyphen – you can't put spaces within variable names). Then click the value box.

  49. We want to define male-gamete as the product of meiosis working on male-genotype. You can bring down a Meiosis box into the value box, but it's easier to cut/paste the box you already have. Mouse over the Action Icon of the Meiosis function in the Workspace.

  50. …and click cut.

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