BIMM 141 - Introduction to Bioinformatics - Spring 2001

Exercise 1 - Key

My comments look like this ... Total Score: xxx pts

Note: Student files may be in the student home directory (bi141s**) or in subdirectories exer1_manager or exer1 .... you need to look in all of these directories for the files...

Summary of Grading:	Points
A. Use of Unix Computers:	10 pts
1. Into to Unix Computers: Sun Ultra 10	6 pts
2. Intro to Gateway + Linux and SGI Iris	6 pts
3. Intro to vi Editor	3 pts
4. Standard Unix commands	pts
a. Your Account: pwd, ls -alF, man	15 pts
b. Files and Subdirectories: vi, cat, mkdir	12 pts
c. Moving betwen Subdirectories: mv	18 pts
d. Moving, Copying, and Deleting Files: mv, cp, rm	22 pts
e. Interactions with Other Computers: telnet, rlogin, ftp	40 pts
B2. Saving Images from the Web	6 pts
C. Questions	122 pts
Total	260 pts

 

{A. Use of Unix Computers}

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

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

{b. Get the Template for Exercise 1 as an .html file in your Account}
3 pts ... did all this ...

{1) Turn on Netscape Communicator}
did this ...

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

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

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

{1) Turn on Netscape (NS) Composer}
did this ...

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

{d. Begin to do Exercise 1}

{e. Do the Tutorial "Introducing Your Desktop}
1 pts, more points for Questions answered at end ... did this ...

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

{f. Do the Tutorial on "Moving Text"}
1 pts ... did this ...

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

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

{1) Explore elements of the Help facility}
looked aroung in the Help facility some ...

{2) Create new Console windows using each of Three Methods}
The easiest way to do this with the Sun CDE is to place the mouse on the background, click the mouse right button, and choose Terminal or Console under the Programs menu.
 
 

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

{a. Gateway Linux Computers}
3 pts ... did this ...

{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}
3 pts ... did this ...

{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}
3 pts ... did this ... The file exer1.vi should be examined in the student account, to see that they did this ...

{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}
3 pts ... pwd shows the current working directory

{At the % prompt, do: ls}
3 pts ... ls lists the names of files in the current working directory that are not dot files

{At the % prompt, do: man ls}
3 pts ... man ls invokes the Unix manual, with a description appearing of the ls command and all of its options

{At the % prompt, do: ls -al}
3 pts ... ls -al lists files with the "a" and "l" options: a - list ALL files; l - do "long" listing, with permissions, etc info shown as well as file name

{At the % prompt, do: ls -alF}
3 pts ... ls -alF does ls -al plus the F option: shows subdirectories via /, programs via *, etc
 
 

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

{Do at the % prompt: cat > short.txt}
3 pts ... This command creates file short.txt and permits entry of text into the file. I did this for 3-4 lines and then stop editing and closed the file via Ctrl-D command.
Hiren: this file should be in the student account ... check this out ...

{Now do at the % prompt: cat short.txt}
3 pts ... Since the file short.txt now exists, the cat commands will display the contents of the file.

{At the % prompt, do: mkdir exer1}
3 pts ... This creates a new subdirectory called exer1

{At the % prompt, do: mkdir exer2}
3 pts ... This creates a second new subdirectory called exer2
 
 

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

{At the % prompt, do: cd exer1_manager}
3 pts ... This cd commands changes the working directory to the exer1_manager directory that was created above during the tutorial on "Managing your Work: Files, Folders"

{At the % prompt, do: cd ..}
3 pts ... This cd command changes directories to the directory immediately above the current directory (the .. directory)

{At the % prompt, do: cd exer2 confirm where you are; do: pwd}
3 pts ... The cd exer2 command changes directory to the exer2 subdirectory created above. The pwd command should show that you are in the exer2 subdirectory.

{Now do at the % prompt: cd ../exer1 confirm where you are; do: pwd}
6 pts ... This cd command first moves to the .. directory, the directory immediately above the current directory, and then moves down to the exer1 directory, a subdirectory of the directory immediately above the current directory. The pwd command should show that you ended up in the exer1 directory.

{At the % prompt, do: cd}
3 pts ... The cd command with no argument returns you to your Home Directory bi141s**.

{confirm where you are; do: pwd}
The pwd command should show that you are in your home directory.
 
 

{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}
The cd command with no argument returns you to your Home Directory bi141s**

{Now do at the % prompt: ls -alF}
1 pts ... This command lists all the files in your current directory bi141s** in long format, with designation of file types such as directories, programs (executables), etc ...

{At the % prompt, do: mv exer1.vi exer1/}
3 pts ... This mv command "moves" file exer1.vi into subdirectory exer1.

{At the % prompt, do: ls -alF}
1 pts ... This command lists all the files in your current directory bi141s** in long format, with designation of file types such as directories, programs (executables), etc ...

{At the % prompt, do: cd exer1}
3 pts ... This command changes directory to subdirectory exer1

{do: pwd}
1 pts ... This command shows where you are, that you are in subdirectory exer1

{do: ls -alF}
1 pts ... This command lists all files in subdirectory exer1 in long format with file designations

{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}
3 pts ... This cp copy command copies file exer1_skel.html to subdirectory exer1 and gives the new file a new name exer1.html

{return to your home directory - do: cd}

{At the % prompt, do: cp exer1_skel.html exer1_skel.html-copy}
3 pts ... This cp copy command copies file exer1_skel.html to a new file exer1_skel.html-copy in the same directory.

{Now do at the % prompt: cp exer1_skel.html-copy exer1/}
3 pts ... This cp command makes a copy of file exer1_skel.html-copy in subdirectory exer1 and gives the new file the same name as the old file.
 
 

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

{At the % prompt, do: rm exer1_skel.html-copy}
3 pts ... This rm remove or delete command deletes the file exer1_skel.html-copy from the current directory
 
 

{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}
3 pts ... This telnet commands permits you to access and login to your account on a second computer, here the computer phcomp which is the server for the Gateway Linux computers in 4306 York Hall.

{At the % prompt, type: rlogin nssgi-1}
5 pts ... The rlogin command is very similar to the telnet command, and here you are logging into computer nssgi-1 from the computer where you currently are, namely computer phcomp.

{At the % prompt, type: logout}
2 pts ... This logout command logs you out of the third computer, the nssgi-1 computer

{At the % prompt, again type: logout}
2 pts ... This logout command logs you out of the second computer, the phcomp computer
 
 

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

{At the % prompt on a Sun computer, type: ftp phcomp}
3 pts ... This ftp command is logging you into a second computer phcomp and establishing the software protocol (file trabsfer protocol) to permit you to transfer files between the two computers.

{At the ftp> prompt, do: ?}
3 pts ... This ? brings up a display of all the implemented ftp commands. To see what any given command <command> does, you can do at the ftp> prompt: help <command>

{At the ftp> prompt, do: pwd}
1 pts ... This ftp command pwd shows the current working directoy on the second computer.

{At the ftp> prompt, do: ls}
1 pts ... This ftp comannd lists the files (all but the. files) present in directory on the second computer.

{At the ftp> prompt, do: binary}
3 pts ... The binary command sets the ftp software to transfer files using binary (machine language) format

{At the ftp> prompt, do: ascii}
3 pts ... The ascii command sets the ftp software to transfer files using ascii (text) format

{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}
3 pts ... The put command puts a copy of the file of name <filename> present on the first computer into the current directory on the second computer

{At the ftp> prompt, do: ls}
1 pts ... The ls command here lists the files present in the current directory on the second computer, and should now include the file you transferred in the step above.

{At the ftp> prompt, do: rename <filename> <new_filename>}
3 pts ... This ftp command rename, different from the Unix command mv, gives a new name <new filename> to the file that initially has the name <filename>

{At the ftp> prompt, do: ls}
1 pts ... The ls command here lists the files present in the current directory on the second computer, and should now include the file <new filename>, the file you renamed in the step above. The file of name <filename> should now be missing.

{At the ftp> prompt, do: get <new_filename>}
3 pts ... This ftp command get transfers a file, in this case of name <new filename>, from the second computer to the first computer.

{At the ftp> prompt, do: quit}
3 pts ... This quit commands causes you to leave the ftp> program and returns you to the Unix % prompt.
 
 

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

{At the % prompt, do: date"}
3 pts ... The date command displays the current date and time.

{At the % prompt, do: who"}
3 pts ... The who command lists all users who are logged onto your same Unix computer.
The command finger does similarly.

{At the % prompt, do: logout"}
3 pts ... The logout command logs you out of your account. On the Unix computers in 4306 York, you need to also logout or exit from the computer as a whole.
 
 
 
 

{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}
did this ...

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

{c. Save image in your directory exer1}
3 pts ... did this ...

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

{e. Choose Browse to find your *.gif file, choose this, and click ok }
3 pts ... did this, as you should be able to see right here ...
 
 
 
 

{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?

3 pts ... These are in general a Console or xterm window, a Help window, and a Desktop Environment window.

 

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

2 pts ... The computer is insci14 from the Sun computers. It is a Unix server located elsewhere (probably in AP&M) acting as a server for the 16 Sun computers in 4306 York ...

 

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

2 pts ... The home directory is the directory you enter when you log on. It has the same name as your Username or Account Name. An example is bi141sab

 

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

2 pts ... Netscape Communicator is an Internet program that is comprised of other programs. Netscape Navigator is the Web browser program within Netscape Communicator. Internet Explorer is simply a Web browser, and hence more closely resembles Netscape Navigator.

 

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?

1 pts ... http://www.sdsc.edu/~gribskov/bimm140/

 

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

2 pts ... The template file provides the instructions for the Exercise, and permits students to do an Exercise via a "fill in the blanks" style

 

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

3 pts ... The three windows conveniently used are: 1) the complete Exercise opened in a Netscape Navigator window; 2) the Lab Notebook under construction for the Exercise in a Netscape Composer window; and 3) a third window appropriate for the task being performed, eg a Console window for Unix commands or a second Netscape Navigator window for use of the Web

 

8. What does the Netscape Composer program do?

2 pts ... Netscape Composer is a Web page editor, permitting the writing and editing of html files for use on the Web.

 

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?

3 pts ... The left button is the standard mouse button for most mouse tasks. The right button is used for speialized tasks such as bringing up a pop-up menu from the background. The middle button is also used for specialized tasks such as pasting text within the vi editor.

 

2. What is a window?

2 pts ... A window is an object on the monitor screen displaying the output of some software program such as a Netscape window, a console window (the command line Unix software), the Common Desktop Environment window, a text editor window.

 

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

2 pts ... To close a window on a Unix computer usually means to minimize its size or to 'iconize' it, ie convert the window into an icon which then is usually found on some edge of the screen. This closed window can be opened again by double-clicking on the icon.

To quit a window means to permanently close the 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?

2 pts ... This operation brings up a pop-down menu providing a variety of options
    b. double-click in the upper bar of the window?

2 pts ... This operation does nothing in the CDE, but expands the window vertically to the height of the monitor in the OpenWindows environment
    c. place the mouse cursor in the lower right corner, click, and move the cursor with the mouse?
2 pts ... This operation resizes the window, with the bottom right corner of the window ending up whereever the mouse was at the time the 'click' was released.
    d. click on one of the arrows of either the horizontal or vertical
2 pts ... This causes the part of the file displayed in the window to move, up or down vertically, or right or left horizontally.
 

5. How do you move a window?
2 pts ... Place the mouse cursor on the top bar of the window, click and hold, and move the mouse.  The window moves with the mouse.
 

6. How do you move a window forward ahead of another window?
2 pts ... Click  once  anywhere in a given window; it moves to the front.
 

7. How do you move a window backward behind another window?
2 pts ... TBy moving the other window ahead of the first window (by clicking anywhere in the other window).
 

8. How do you resize a window?
2 pts ... Move the mouse cursor to any of the four edges of a window, until the cursor changes shape.  Click and hold, then drag the cursor; the window will change size and shape.  To resize vertically and horizontally at the same time, move the mouse cursor to the lowere right corner of a window, until it changes shape.  Click and hold, and drag the cursor; the window will resize, with the bottom right corner of the window ending up whereever the mouse was at the time the 'click' was released.
 

9. What are the seven operations for using the Scrollbar to move through a document?
3 pts ... In the CDE, there are only five clicking operations: the two arrows (window scrolls continuously), the dark space above and below the scroll bar (window scrolls one page at a time), and the scroll bar (window scrolls to position where scroll bar is placed).  In OpenWindows, the two arrows are part of the scroll bar; two additional operations occur by clicking in the rectangles at either end of the scroll bar (move to top or bottom - or right or left end - of document displayed).

10. Are there any differences in these operations between Vertical and Horizontal Scrollbars?
1 pts ... No
 

11. What is a popup menu?
2 pts ... A popup menu is one that appears or 'pops up' upon some operation such as moving the mouse cursor over the CDE background or over any open window, and clicking with the right mouse button.
 

12. Which button of the mouse brings up popup menus?
2 pts ... the right  button usually
 

13. Are the popup menus the same for different windows?
2 pts ... No ... they reflect the properties of the tasks performed by the software displayed in the window.
 

14. What are submenus?
2 pts ... Submenus are additional menus reached via a primary menu.  The primary menu will have arrows associated with any menu item that has a submenu.
 

15. What is the workspace?
2 pts ... The workspace is the total area displayed by the monitor.
 

16. What is the workspace menu?
2 pts ... The workspace menu is the popup menu that appears when one places the mouse cursor on the background and clicks the right button of the mouse.
 

17. What does "pinning the workspace menu" mean?
2 pts ... In the OpenWindows Environment, when one executes a choice from the workspace menu, the menu then disappears.  To prevent it from disappearing, one can click on the 'pin' icon at the top of the

menu. Such 'pinning' capability is not present in the Common Desk Environment.

 

10. Questions on "Moving Text":

1. What are the keyboard commands for text COPY, text CUT, text PASTE?
3 pts ... In the CDE, the commands are alt-C for COPY, alt-X for CUT, and alt-V for PASTE.

2. How do these commands compare with those typically used on PC and Mac computers?
1 pts ... They are very similar.  On Mac computers, the commands are command-C for COPY, command-X for CUT, and command-V for PASTE.
 

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

1. What is the difference between a folder and a subdirectory?
1 pts ... There is no 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 pts ... The vi editor is the Unix visual text editor used for text editing. visual means that you actually see the text being edited on the screen in front of you, in a more or less wysiwyg manner.

 

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

3 pts ... The two modes are the text entry mode, in which text is added to the contents of the file, and the command mode, in which commands are excuted to move around in the file, to move text within the file, to save and lose the file, etc

 

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

2 pts ... Such is desirable if one runs more than one application from a given xterm or Command Line window simultaneously without running all but one of these applications in the background.

 

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

3 pts ... Netscape Navigator (to read the Exercise), Netscape Composer (to do the Exercise), and a 3rd window with appropriate program, eg Netscape Navigator for Web work or Unix console window for GCG programs, to execute tasks called for by the Exercise.

 

15. What does "pinning" of a Menu on a Sun Unix machine do?
2 pts ... In the OpenWindows environment, pinning causes a window to remain on the screen. Without such pinning, the window disappears after the first use of the window.

 

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

3 pts ... These 'Utility' programs are those found under Unix (grep, awk, mail, ...) plus some others (clock, calendar, calculator, ...)

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

2 pts ... X-Windows programs are those that have graphics components that run under the X-Windows graphics standard.

 

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

2 pts ... pwd states what the current working directory is
File Manager: look at the name of the directory

ls -al
2 pts ... ls -al lists all files in a directory, including hidden dot files, in long format, with previleges, size, date of last modification, etc.  In File Manager: ls can be  by any of the View Options.  However, to get ls -al, one must select Show hidden objects and display or view by list including Name, date, size, ...

mkdir subdir1
2 pts ... This command creates a subdirectory subdir1.  File Manager: in the File pulldown menu, select New folder ... and give it the name subdir1

cd ..
2 pts ... This changes the working directory to be the directory immediately above the current working directory.  File Manager: in the File menu, select Go Up

cd ../../subdir3
2 pts ... This command also changes the working directory, by going up two in the directory tree, and down into subdir2.  File Manager: select Go Up twice from the File menu, then double-click with the left mouse button on the subdirectory subdir3

cp file1 ../../subdir3/file1.backup
2 pts ... This command copies a file file1 to the subdir3 subdirectory and renames the new file as file file1.backup.  File Manager: select file file1 and then choose the Copy to ... command from the Selected pulldown menu.  This brings up a popup menu called the File Manager - Copy Object.  As Destination Folder, go up two, remove these, and go down one by typing in subdir3.  In the Name for copy: box, type in file1.backup  Click OK

mv file1 ../../subdir3/file1.backup
2 pts ... This command moves a file file1 to the subdir3 subdirectory and renames the new file as file file1.backup.  File Manager: select file file1 and then choose the Move to ... command from the Selected pulldown menu.  This brings up a popup menu called the File Manager - Move Object.  As Destination Folder, go up two, remove these, and go down one by typing in subdir3.  Click OK
The mouse can also be used for this operation via 'DRAG-DROP' operations

who
2 pts ... This WHO command shows who is currently logged onto this computer.  File Manager: I don't think one can execute this command from the File Manager

logout
2 pts ... This commands logs the user off the computer.  File Manager: choose Log out... from the Programs choice of the popup menu that appears when the mouse is right clicked on the background of the workspace.

 

18. What happened when you executed the Unix command: telnet phcomp?
2 pts ... Connection was made to the computer phcomp.

19. What computer were you logged into after you logged in?
2 pts ... You were logged into computer phcomp

 

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

2 pts ... You would have been connected up and logged into computer nssgi-1.

 

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

2 pts ... The prompt was that associated with computer phcomp

 

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

2 pts ... After the first logout, you returned to phcomp. After the second logout, you returned to insci14.

 

23. Name two ftp commands that are identical to Unix commands and two which are different.
2 pts ... Two that are identical: ls and pwd. Two that are different: rename and get

 

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

2 pts ... The two primary ftp commands are those that transfer files put (transfer files from the original computer to the one into which you ftp connected) and get (transfer files from the second computer to the original computer)

 

25. What is the Internet?
2 pts ... The Internet is a network coupled with software that permits files on different computers from all over the world to interact with each other. The network is physical wiring: coax cable, twisted pair, fiber optics ... and now wireless. The software is based on the Markup Language called HTML (HyperText Markup Language); this language together with concepts of URL permit the interaction between computers.

 

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

2 pts ... Bioinformatics resources (databases, software, information) take advantage of the Internet to provide connectivity and interaction between computers, each of which contain Bioinformatics resources created by users of these specific computers and facilities. Hence, the Internet is crucial to a course providing an Introduction to Bioinformatics, the subject matter of BIMM 140 and 141.

 

27. What is a "federated collection of databases", and why is use of such a collection of importance in modern-day molecular biology?
2 pts ... A federated collection of databases is a group of databases, of different types created by different people and housed and maintained in different locations throughout the world. This collection is of importance in modern molecular biology because the information contained is crucial to the design of further experiments and to the interpretation of data from performed experiments. This information is not on only one computer or in one location, but is found throughout the world, accessed via the Internet.

 

28. What is "whole genome" biology?
2 pts ... Whole Genome biology is the biology that emerges when one has knowledge of the nucleotide sequence of the whole geneome.

 

29. What is a "gif image"?
2 pts ... A gif image is an image which is formatted in the GIF (Graphics Interchange Format) format. It is supported by essentially all Web browsers and is particularly good for images of high contrast, such as text images. Files in the GIF format are in general comparatively small files.