BIMM 141 - Exer1_Skel - Spring, 2001

Exercise 1

{A. Use of Unix Computers}

{1. Introcution to Unix Compters: Sun Ultra10 Unix Computers}

{a. Bring the computer out of 'sleep' mode by pressing any key and logon}

{b. Get the Template for Exercise 1 as an .html file in your Account}

{1) Turn on Netscape Communicator}

{2) Go to BIMM 141 Exercises Web page in a new NS Navigator window}

{3) Get a copy of the Exercise 1 Template File}

{c. Use NS Composer in Netscape Communicator to do Exercise 1}

{1) Turn on Netscape (NS) Composer}

{2) Bring up the Template for Exercise 1 in NS Composer}

{d. Begin to do Exercise 1}

{e. Do the Tutorial "Introducing Your Desktop}

{Do the Help Tutorial on "Controlling the Mouse and Using Unix Windows"}

{f. Do the Tutorial on "Moving Text"}

{g. Do the Tutorial on "Managing your Work: Files, Folders"}

{h. Opening additional Console or Command Line Windows, and Help in general}

{1) Explore elements of the Help facility}

{2) Create new Console windows using each of Three Methods}

{2. Introduction to the Gateway Linux and SGI O2 Unix Computers}

{a. Gateway Linux Computers}

{1) Login to a Gateway Linux Computer in the KDE Windows Environment}

{2) Examine the Icons at the bottom of the Screen}

{3) Quickly go through the Tutorial "A Quick Start Guide to the Desktop"}

{b. Silicon Graphics (SGI) Iris O2 Computers}

{1) Login to an SGI O2 Iris Computer}

{2) Examine the Options in the Toolchest}

{3) Examine the Options under Help in the Desktop}

{3. Introduction to the Unix vi Editor}

{a. Create a file called exer1.vi using the vi Editor}

{4.Use of standard Unix commands at Command Line prompt}

{a. Unix commands and Your Account: pwd, ls -alF, man}

{Briefly describe in your Lab Notebook what happens with each of the following operations}

{At the % prompt, do: pwd}

{At the % prompt, do: ls}

{At the % prompt, do: man ls}

{At the % prompt, do: ls -al}

{At the % prompt, do: ls -alF}

{b. Unix commands and Creating Text Files and Subdirectories: vi, cat, mkdir}

{Do at the % prompt: cat > short.txt}

{Now do at the % prompt: cat short.txt}

{At the % prompt, do: mkdir exer1}

{At the % prompt, do: mkdir exer2}

{c. Unix commands and Moving between Subdirectories: cd}

{At the % prompt, do: cd exer1_manager}

{At the % prompt, do: cd ..}

{At the % prompt, do: cd exer2 confirm where you are; do: pwd}

{Now do at the % prompt: cd ../exer1 confirm where you are; do: pwd}

{At the % prompt, do: cd}

{confirm where you are; do: pwd}

{d. Unix commands and Renaming, Moving, Copying, and Deleting Files: mv, cp, rm}

{1) Use of the Unix mv command to Move a File with no Rename Operation}

{At the % prompt, do: cd}

{Now do at the % prompt: ls -alF}

{At the % prompt, do: mv exer1.vi exer1/}

{At the % prompt, do: ls -alF}

{At the % prompt, do: cd exer1}

{do: pwd}

{do: ls -alF}

{Return to your home directory; do either: cd or do: cd .. and confirm where you are ...}

{2) Use of the Unix cp command to Make a Copy of a File}

{At the % prompt, do: cp exer1_skel.html exer1/exer1.html}

{return to your home directory - do: cd}

{At the % prompt, do: cp exer1_skel.html exer1_skel.html-copy}

{Now do at the % prompt: cp exer1_skel.html-copy exer1/}

{3) Use of the Unix rm command to Remove or Delete Files}

{At the % prompt, do: rm exer1_skel.html-copy}

{e. Unix Commands and Interactions with Other Computers: telnet, rlogin, ftp}

{1) Use of Unix telnet or rlogin Command to Connect to a Second Computer}

{At the % prompt on a Sun computer, type: telnet phcomp}

{At the % prompt, type: rlogin nssgi-1}

{At the % prompt, type: logout}

{At the % prompt, again type: logout}

{2) Use of Unix ftp Command to Transfer Files between Two Computers}

{At the % prompt on a Sun computer, type: ftp phcomp}

{At the ftp> prompt, do: ?}

{At the ftp> prompt, do: pwd}

{At the ftp> prompt, do: ls}

{At the ftp> prompt, do: binary}

{At the ftp> prompt, do: ascii}

{At the ftp> prompt, do: put <filename> where <filename> is the name of a text file you have in your Sun account, eg your Exercise 1 HTML file}

{At the ftp> prompt, do: ls}

{At the ftp> prompt, do: rename <filename> <new_filename>}

{At the ftp> prompt, do: ls}

{At the ftp> prompt, do: get <new_filename>}

{At the ftp> prompt, do: quit}

{f. Additional Useful Unix Commands: date, who, logout}

{At the % prompt, do: date"}

{At the % prompt, do: who"}

{At the % prompt, do: logout"}

{B. Netscape and the Internet}

{1. The DNASYSTEM and CMS MBR Web Sites}

{2. Saving Images for Lab Notebook files}

{a. Place mouse cursor over image in Netscape window}

{b. Click right mouse button and select: Save image as ... }

{c. Save image in your directory exer1}

{d. From the Insert pull-down menu in Netscape Composer, choose Image }

{e. Choose Browse to find your *.gif file, choose this, and click ok }

{C. Questions:}

{Answer all of the following questions:}

1. What are the three Windows that appear when you log on to a Sun computer in 4306 Urey Hall?

2. What computer are you logged onto? How is this computer related to those in 4306 Urey Hall?

3. What is your home directory and what does this terminology mean?

4. How does Netscape Communicator differ from Netscape Navigator? Which most closely resembles Internet Explorer?

5. The BIMM 140/141 home page is the primary method of providing updated information to BIMM 140/141 students. What is the URL for the BIMM 140/141 home page?

6. What is the purpose of the Template file for each of the BIMM 141 Exercises?

7. What is the purpose of each of the three windows that you work with when doing a BIMM 141 Exercise?

8. What does the Netscape Composer program do?

9. Questions from Tutorial on "Controlling the Mouse and Using Windows":

1. What are the three buttons of the Unix mouse, and what is each used for?

2. What is a window?

3. What is the difference between 'close a window' and 'quit a window'?

4.What happens if with the Mouse left button you:
    a. click in the small square in the upper left corner of a window?
    b. double-click in the upper bar of the window?
    c. place the mouse cursur in the lower right corner, click, and move the cursor with the mouse?
    d. click on one of the arrows of either the horizontal or vertical

5. How do you move a window?

6. How do you move a window forward ahead of another window?

7. How do you move a window backward behind another window?

8. How do you resize a window?

9. What are the seven operations for using the Scrollbar to move through a document?

10. Are there any differences in these operations between Vertical and Horizontal Scrollbars?

11. What is a popup menu?

12. Which button of the mouse brings up popup menus?

13. Are the popup menus the same for different windows?

14. What are submenus?

15. What is the workspace?

16. What is the workspace menu?

17. What does "pinning the workspace menu" mean?

10. Questions on "Moving Text":

1. What are the keyboard commands for text COPY, text CUT, text PASTE?

2. How do these commands compare with those typically used on PC and Mac computers?

11. Questions on "Managing your Work: Files, Folders":

1. What is the difference between a folder and a subdirectory?

12. Questions on the Unix vi Editor:

1. What is the vi editor used for? vi stands for "VIsual"; how is this editor "visual"?

2. What are the two modes of the vi editor, and what is each used for?

13. Why is it often desirable to have more than one Command Line window opened simultaneously?

14. Commonly, in doing Exercises for BIMM 141, what three types of programs will you be running simultaneously on your Unix machine?

15. What does "pinning" of a Menu on a Sun Unix machine do?

16. What are some of the File Manager "Utility" programs available?

Note that these are X-Windows programs; what does this mean?

17. Briefly describe the function of each of the following Unix commands and state what the comparable operation using the Sun Unix File Manager would be:

pwd

ls -al

mkdir subdir1

cd ..

cd ../../subdir3

cp file1 ../../subdir3/file1.backup

mv file1 ../../subdir3/file1.backup

who

logout

18. What happened when you executed the Unix command: telnet phcomp?

19. What computer were you logged into after you logged in?

20. What would have happened if you had executed: rlogin nssgi-1?

21. What was the new prompt after you executed the Unix command: telnet phcomp?

22. What computer were you are on in your telnet session after the first logout? after the second logout?

23. Name two ftp commands that are identical to Unix commands and two which are different.

24. What are the two primary ftp commands and what do they do?

25. What is the Internet?

26. How is the Internet important to these two courses BIMM 140 and BIMM 141?

27. What is a "federated collection of databases", and why is use of such a collection of importance in modern-day molecular biology?

28. What is "whole genome" biology?

29. What is a "gif image"?