A basic introduction to the computing platforms on which this course will be taught. Items covered include background information on computers, the nature of computing resources to be used, and instructions on using a text editor.
Author:
Susan Jean Johns
An Introduction to Computers
One dictionary definition of a computer is "an electronic machine that performs rapid, complex calculations, or compiles and correlates data." This definition leaves to one's imagination the actual parts of the electronic machine.
A computer is composed of five basic parts: a processor for doing calculations, a data input device (such as a keyboard), a data output device (such as a monitor screen), a data storage device (such as floppy disks or a hard drive) and memory to provide space for the computing process to take place. The size of these components and their speed determines whether the computer is a personal, a micro, a mini, a mainframe or a super computer. WSU has all these types of computers on campus except for a super computer. Individuals with needs for super computing time have to apply for time at national super computing facilities.
Computers have all sorts of combinations of these five basic components. Normally the data input and output devices are combined into a device known as a terminal. Terminals have a video screen and a keyboard for data entry. Older styles of terminals have the screen and keyboard all in the same cabinet, newer ones have the keyboard detached to help reduce user fatigue. Older style computers had all the components in separate boxes connected by cables. Newer machines may have everything in one box or the processor, storage and memory components in one box with an associated terminal (monitor).
Computers have a set of commands which allow them to perform their various tasks, known as an operating system. While the functions that various computers perform are similar, the names given to functions vary from one type of machine to another. The way in which these commands are entered also vary. The Macintosh is designed to be used mostly with a mouse from a series of menus, while other systems may depend on keyboard entries.
Computers may be either stand-alone units or be connected to other machines. A stand-alone unit is self-contained, needing no other machine to do its computing tasks. Such machines are limited only by software constraints, processor speed and memory size. There are times when one computer must communicate with another computer or even pretend to be a simple terminal on that second machine. When a computer pretends to be a terminal it is called terminal emulation. Usually software is required for a stand-alone machine to do this function. Through terminal emulation, a personal computer can serve as a terminal device on a much larger machine which has software or computing capabilities that the personal computer does not possess itself. Information can also be passed from one machine to another during this process, saving the necessity of re-entering the same data on two different machines.
Computers only do what they have been programmed to do. Their accuracy in any given task depends on the thoroughness and completeness of the software being used and the manner in which it is used. In scientific research, this means that the accuracy of your results depends on your understanding of the strengths and weaknesses of the software being used, and how well you interpret the produced results.
BC/BP 578 will be taught using the equipment located in 210 Commons. This area is known as the VADMS Teaching Laboratory. The bulk of the computer equipment located here was upgraded in part by Virtual WSU funds.
These machines are MAC Power PC clones. When the screen saver is not in effect the following image appears on the screen. It lists the locally available software on the machine in the standard icon-window format.
Of the software listed in the Launcher window, NETSCAPE, RIBOZYME, MODEL1 and X RIBOZYME will be used most. Netscape is the course's web browser. A number of biocomputing resources are only available on the web. Two of the others are standard terminal emulator means of connecting to the VADMS' computers, ribozyme and model1. This emulation allows the clones to act like Tektronix's color graphics terminals and use software that calls for that type of graphical output. X RIBOZYME is the x-window emulator means of connecting to ribozyme and is used when x-windowing software is run on that platform.
In this course the clones serve a number of purposes. First, they run software located on the machines themselves. Second, they serve as terminal emulators. This means that the clones pretend to be terminals connected to another machine and do not use their own computing resources to perform computing tasks.
BC/BP 578 relies on the computing resources of the VADMS Center. These resources are housed on the VADMS' platforms. These machines will serve as the hosts for the clones. To connect to these resources, the clones must communicate with their host machines over a network. For connecting to a host, these machines normally use Versa Term Pro for terminal emulation.
Emulators affect the way a device (in this case the clone) communicates with its host machine (the VADMS machines). They make it possible to change the functions of the keyboard's keys. Since the computer pretends to be another type of terminal, the keyboard setup must match that of the original terminal. Many terminals have their own distinct keyboard layouts. Changing the keys' functions to match those of another keyboard is known as remapping. Depending on the terminal being emulated, you may need more than one set of remapped keys. Some terminals use the same keys for different purposes in general operation as opposed to editing tasks. The clones are set up to act like VT220 terminals, a generic ascii terminal type.
The computing platforms you will use are VADMS platforms. These machines have their own way of managing users and the portion of the computer they are allowed to work in, and their own distinct operating system, command language, filename conventions, online help and batch facilities.
Both are multi-user systems. Users work in individual portions of the machine's resources called accounts.
-------------------------------------------------------------------------------- | account | | | | account - a term used to describe the working space of a user on a computer. | | This is where the user's files are stored. This term can also mean the name | | given to a user's working space for management purposes. | --------------------------------------------------------------------------------
Each account has associated with it a username and a password that allows access to this working space. Accounts are allocated a number of blocks to work in on one of computer's many storage disks. Each account has a number of privileges associated with it that control access to other accounts' files, networking devices, and mail functions.
VADMS' machines have two different operating systems. Ribozyme uses the SGI version of UNIX called IRIX and model1 uses the VMS operating system. Both are command line-driven operating systems. The commands that operate the machine are entered after the machine's prompt. Such a system is very sensitive to typing errors. There are no pull-down windows or menus on these machines unless you are operating in an X-windowing environment.
The bulk of your computing tasks will be done on ribozyme. Therefore, in this early part of the course, emphasis will be placed on learning how to function in the IRIX version of the UNIX world. Those students selecting a molecular modelling project will become familiar with both operating systems, IRIX and VMS. The software that permits actual structure data entry is on a platform running a VMS operating system.
--------------------------------------------------------------------------------- | filename conventions | | | | filename - a term used to describe the actual name of a file. Filenames are | | usually composed of two parts. The first part of the filename is the name of | | the file, the second part is the extension name. The two parts are separated | | by a period. | | | | extension | | | | extension - a term used to describe the second part of the filename of a file.| | Extensions can also be used to denote certain types of data, or information | | from given data sources. | ---------------------------------------------------------------------------------
Ribozyme has an online help feature that can be both helpful and frustrating. You need to know the term you want information on before you can look anything up about it. This usually means conferring with a UNIX text of some sort. By typing man (for manual) and the term you want more information on, the machine will show you what it has online about that particular term. Beware, examples of how to use a term or function are usually not given in these manual pages.
Ribozyme can perform batch processing tasks. The machine is set up to respond to the needs of interactive users (those currently logged onto the machine and busily working) as its first priority. However, if these users are not completely occupying the device, batch processes (tasks being run for users not currently logged on) will be given the unused portion of the device. Batch processes are controlled by queues which have different priority levels and lengths of processing time. Queues operate on a first come, first served basis.
Accessing Ribozyme Information
A graphics emulator program called Versa Term Pro has been installed on the clones. This allows you to access a VADMS' platform and run graphical software on that device. It uses networking software as its carrier to make contact with the desired machine.
l) Activating the computer
The clones are always on. When they have not been used for some time a screen saver comes on. Press any key to change the terminal from screen saver mode to active. The activated machine displays Launcher window screen given on page 3.
2) Select the RIBOZYME icon
From the window, select the RIBOZYME icon by moving the cursor arrow with the mouse over to the RIBOZYME icon and pressing the mouse button twice.
Successful connection to ribozyme is denoted by the appearance of a ribozyme information line and a login: prompt.
IRIX (ribozyme) login:
After you enter your account name, the machine prompts you to enter your account's password.
Password:
The current intro message from ribozyme is given on the next page.
IRIX Release 6.2 IP21 ribozyme
Copyright 1987-1996 Silicon Graphics, Inc. All Rights Reserved.
Last login: Mon Jan 10 13:17:55 PST 1997 by UNKNOWN@clone2.vadms.wsu.edu
This is a Power Challenge L running IRIX 6.2
Sequence analysis users, may enter the term seqtool to get into the
character driven menuing system for access to VADMS sequencing software.
Use pico for editing and pine for mail.
The EST files have been separated out of GenEmbl. Use est:* for the
database if you want to search this information.
Please note that changes in the BLAST menu. Searching only GENBANK or
EMBL is no longer possible.
A new solution to the font problem in PHYLIP has been created. If you are
interested, check out the following file" $PHYLIP_DIR/font.readme
VADMS' Web page URL:
Mosaic users http://ribozyme.vadms.wsu.edu/~vadms/
Netscape users http://www.vadms.wsu.edu/
You are into your account when you have seen the intro message and the machine returns to you the % prompt.
Each BC/BP 578 student will use his or her own account with the initial password mygenes0. Students in this class have one of the stock usernames created specifically for the course. You will be assigned one of these account names by your instructors to use for the duration of the class. Record that account name below.
account name: ________________________________________________________
All account names on ribozyme are in lower case letters. The password will not be shown on the screen, so enter it carefully. Once in your account, you need to be very sensitive about typing upper and lower case characters. UNIX operating systems treat these characters differently.
A general welcome to ribozyme will appear on the screen, showing the version of its operating system and any messages of general interest.
To log off ribozyme, enter the term logout. You will be automatically logged out of your account.
% logout
Although you are now off ribozyme, you still need to get out of the emulator you were using. Move the arrow to the File portion of the control bar at the top of the screen. Holding the mouse button down, select the Quit option from the menu and then release the mouse button. The screen will return to the Launcher window.
Week 2 Exercise
The purpose of this series of exercises is to acquaint you with accessing ribozyme, learning something about its operating system, and becoming familiar with editing on the machine. Items in these instructions which appear in bold should be entered followed by pressing the RETURN key.
l) Activating the computer
The clones are always on. Pressing any key changes terminal from screen saver mode to active. The activated machine displays Launcher window screen given on page 3.
2) Select the RIBOZYME icon
From the Launcher window, select the RIBOZYME icon by moving the cursor arrow with the mouse over to the RIBOZYME icon and pressing the mouse button twice. Successful connection to ribozyme is denoted by the appearance of a ribozyme information line and a login: prompt.
IRIX (ribozyme) login:
Once the login: prompt appears, enter your account name to the login: prompt, and then your password to the Password: prompt. This time the password is mygenes0.
Now that you are on ribozyme, it is time to explore its operating system. To do this, you will go through a number of steps designed to give you insight into how this computer works. The prompt on this machine is ribozyme x%. The x demotes the number of the command to be entered next. Throughout this course only the % will be used to show the machine prompt.
4) Change your password.
Change your password to something that you can easily remember that is at least six letters long with at least one numeral. An example of a possible password is froggy3.
% passwd Changing password for bcsxx Old password: enter your old password. New password: what you want the new password to be. Re-enter new password: repeat the new password.
Please record this new password as no one else will know what it is. If you completely forget your password, you will have to contact your lab instructor to have a new password established for your account.
Record your new password in space provided below.
password:_______________________________________________________________
Now that you have protected your account from the prying eyes of others, let's go on to the other aspects of ribozyme's IRIX operating environment.
5) Finding out information about your new computer world.
To gather information about the ribozyme computer environment, a user employs IRIX commands. IRIX is SGI's versions of UNIX. These commands may act independently, or on a number of terms to produce the desired results. The commands often have switches to modify the nature of the produced output.
Computers can tell you the time, but they have a tradition of never being set correctly or of agreeing with one another. At times they may show you the correct time or be an hour off depending on whether the person managing the system has kept up with the latest time change. Some computers have the correct time but don't give the correct year.
% date
The date and time are displayed on the terminal. Record that information below.
time: ____________________________________________________________________
Successful computing requires the use of subdirectories to help keep data being worked on separated from one another. It is easy for users to become confused as to where they are in their account at any one time. The following command, pwd, lets you know where you are in the directory structure of the disk your data is being stored on. This directory pathway is usually much longer than you are aware of due to the way the computer has been set up. In UNIX, subdirectories are denoted by slashes. All the student accounts have been placed in the following directory location, /disk3/usr/local/people. Your resulting path would be one step down from this location on the disk. Record your pwd results below.
% pwd
pwd results: _____________________________________________________________
To separate data into working areas, it is necessary to create subdirectories. This is done with the mkdir command. You use this command with the name of the new subdirectory you want to subdivide your working space. Create the following subdirectory in your account.
% mkdir week2
To see if this command really worked, you need to know how to display the contents of your account and how to interpret the results. This is done with variations on the command, ls.
% ls
The results from this command are similar to that given below.
6lyz.ps mail mx.ps week2
The first and third of these files are the graphics files you looked at during the x-windowing resources tour last week. Your new subdirectory is there, but can you tell if it is a subdirectory of just another file? To find out if a listed file is really a file or a directory, you need to use a more complete form of the ls command, ls -la.
% ls -la
When you enter this command, the following type of output appears on the screen.
total 362
drwxr-xr-x 3 bcsxx class 512 Xxx xx xx:xx .
drwxr-xr-x 4 root sys 512 Xxx xx xx:xx ..
-rw-r--r-- 1 bcsxx class 0 Jan 23 1996 .addressbook
-rw-r--r-- 1 bcsxx class 1257 Jan 23 1996 .addressbook.lu
-rw-r--r-- 1 bcsxx class 550 Jan 22 1996 .cshrc
-rw-r--r-- 1 bcsxx class 652 Jan 22 1996 .gopherrc
-rw-r--r-- 1 bcsxx class 816 Jan 23 1996 .login
-rw-r--r-- 1 bcsxx class 6716 Xxx xx xx:xx .pine-debug1
-rw-r--r-- 1 bcsxx class 10351 Xxx xx xx:xx .pinerc
-rw-r--r-- 1 bcsxx class 722 Jan 22 1996 .profile
-rw-r--r-- 1 bcsxx class 74062 Dec 7 1995 6lyz.ps
-rw-r--r-- 1 bcsxx class 512 Dec 7 08:47 mail
rw-r--r-- 1 bcsxx class 104999 Dec 7 1995 mx.ps
drwxr-xr-x 2 bcsxx class 512 Jan xx 14:01 week2
Notice that there are more files than were shown before. In UNIX there is a
hierarchy of filenames. Those beginning with a period such as .cshrc
are considered to be generated by the system and are not really meant to be
changed by the user. The period serves to hide them during general ls
directory listings. The nature of the file and its protection is given on the
left end of the line, while the name of the file is at the far right end.
There are other changes from the previous directory listing. Notice the d's at the start of some of the entry lines. The letter d at the very left-hand side of an entry line is the way in which a directory is denoted. There are three of them is this listing. The first two, . and .., are the result of your account being created and result whenever a new subdirectory is generated. The third is the week2 subdirectory that was just created. The other letters behind the d refer to the protections on the file or subdirectory. W means write, r means read and x stands for execute. There are three general groupings of users listed here and the type of access each has to your files, system, owner and world. Right now your files are set up so that others can read them.
Looking over more to the right you will notice that other information is given. The owner of the file is given, bcsxx, and their group, class. Further to the right the sizes of the files are given in bytes. Still further to the right is the date and time that the files were created, and at the far right the name of the file. Notice that there are some 1996 or even 1995 dates for some of your files. This is due to the recycling of accounts from one spring semester to another.
Enter the following command and determine the following pieces of information: the size of your .login file and the date when your account was established (the date of the ., and .. listings). Record this information on the lines below.
% ls -la .login.login file size (in bytes): ____________________________________________________
date your account was established: _____________________________________________
Moving around in a UNIX account can be awkward. Use the command cd to change your directory location. To move to a new location, you enter cd followed by the complete directory path of the new one you want to be in. There are a few shortcuts. Your home directory has the alias of $home. Entering cd $home will return you to this location from anywhere on the machine. So will entering cd then the RETURN key. Entering cd .., moves you back one level in the current directory tree.
Now that you have a subdirectory in your account, move into it by entering the following command.
% cd week2
Check out the contents of this subdirectory by doing a ls -la. Since this location was just created, there should only be the . and .. entry lines in the resulting listing.
UNIX, unlike some other operating systems, won't let you move to a location on the machine that doesn't exist. You will get an error message if such a move is attempted.
The UNIX command cp is used to create a copy of an existing file in a new location, or to make a copy of the same file in the same or a different location under a new filename. There is a file in the teacher account that you can use to practice the cp command with. The file name is match.cmp and it is located in the following directory, $GRAD_DIR/data. The term $GRAD_DIR is an environment variable established to contain data files for this course. Enter the following command line to copy this file into your week2 subdirectory. The period at the end of the line tells it to put the file into the current directory.
% cp $GRAD_DIR/data/match.cmp .
A copy of the match.cmp file is now in your week2 subdirectory. Confirm this for yourself by doing the ls command. You can move files from one location to another while being in a completely different part of the account as long as you give the complete paths for the file to be copied and its final location.
cat is the UNIX command that allows the display of the contents of a file on the screen. Not all files are written to be read by users, some are in machine code which results in a mess on the screen. Only those files composed of the characters found on a terminal keyboard, known as ascii files, can be displayed on the screen. To examine the contents of this file, enter the following:
% cat match.cmp
The contents of the match.cmp file are displayed on the screen. This is a comparison table used in aligning sequences and really won't make much sense to you. The entire file was displayed and the process didn't allow you any real control of the speed of the display process. To have the file display one screen's worth of text at a time, use the more command. An example of this command is given below. After the first screen of material is displayed, the process is stopped and a message like this is shown at the bottom of the screen, --More--(yy%). The yy shows how much of the files has actually be shown so far. By pressing the space bar, the process moves on to display the next screen's worth of data. Beware of pressing the RETURN key when using more, for it only move down the file by a single line of text. It should require pressing the space bar 6 times to get through the entire file.
% more match.cmp
To remove files that are no longer needed, use the rm command. This command is very powerful and doesn't ask to confirm your decision. Once the command is given the selected file(s) are gone forever. If you want to remove file(s) with a little more control, use the special VADMS command del. In the VADMS system, del will cause the computer to confirm that you really do want to remove that file. The computer will ask something like, File match.cmp. Remove ? (yes/no)[no] : If so, respond with y. Remove the match.cmp file that you copied over earlier with the following command:
% del match.cmp
You will be asked to confirm that you want this file to be deleted. Respond with y. The file that was copied over earlier in the session has just been removed.
Now copy over some more files to work with. Do the following command to bring these files over into your week2 subdirectory.
% cp $GRAD_DIR/data/bc578*.txt .
The * is a wild card. Any file starting with bc578 and ending with the txt extension will be found and copied over. There are three files, all starting with bc578 and having the txt extension. The above command copied all three into your week2 directory.
Now do a directory listing of the week2 subdirectory. Record below the names of the files now in that location.
files: _______________________________________________________________
Display the contents of the second of these files on the screen with the cat command.
Since the next step is to print off this file, and everyone else in the course has the same file with the same name in their accounts, rename the bc578hi.txt file to reflect your name by entering a command line similar to that given below, where (your lastname) is your last name.
% cp bc578hi.txt (your lastname).txt
To print off a file on ribozyme, you use the lpr command followed by the name of the file you want to print. There is a printer in the teaching lab where your output will be produced. Each print job will contain the number of pages necessary for the contain the desired file and an extra page with the name of the file, who printed it and some other items. This page is known as a banner page and can be used to separate print jobs.
% lpr (your lastname).txt
You can also find out who is on the machine and what they are doing (interactive processing or batch jobs). Three UNIX commands allow you to do this, w, who and finger. These commands are handy when you want to see if a given user is on the system. Of these commands, who gives the least amount of information, just a listing of the accounts that are currently on the computer, what terminal port they are using and when they logged in. The w command produces more information. It shows how long the platform has been up, a shorter name for the terminal, the name of the internet machine being used to connect to the platform, when the account logged in, if the account is actively being used or not and what they are doing. Examples of who and w screen output are listed below.
% who softp ttyq0 Dec 9 17:43 thompson ttyq7 Dec 7 13:02 % w 5:44pm up 2 days, 10:14, 2 users, load average: 0.02, 0.00, 0.00 User tty from login@ idle JCPU PCPU what softp q0 xtsvadms.net.w 5:43pm w thompson q7 clone1.vadms.w Thu 1pm 2days -
Use the who and w commands to locate a fellow student in the course with whom to engage in the next step of the exercise. Other students in the course will be on a internet machine that starts with clonex.vadms, the x denotes the number of the machine in the teaching lab. Record possible fellow student account names in the space below.
% who % w fellow students: ______________________________________________________ _______________________________________________________________________ _______________________________________________________________________
Once you have a selected fellow student to do some more spying on, use the finger command to collect more information on who the person is and what he or she is doing. This is the way to find out the name of the student. An example screen output is given below.
% finger thompson Login name: thompson In real life: Steve M. Thompson Office: 2010 ITB, 335-0533 Directory: /disk2/usr/local/people/thompson Shell: /disk2/usr/local/soft/gen eral/bin/tcsh On since Dec 7 13:02:45 on ttyq7 from clone1.vadms.wsu.edu 3 days 3 hours Idle Time No Plan.
Use finger to find out the name of a selected student account. In the example command line, bcsxx denotes the student account name you have selected. Record several accounts and student names on the next page.
% finger bcsxx
accounts and student names: _____________________________________________
____________________________________________________________________
Now that you have found a person to communicate with, it is time to learn about the UNIX utility talk. Online communications with another ribozyme user is possible through the talk utility. To talk another user enter the following command where username is the account name you want to call.
% talk username
You will get the following type of message on your screen as contact is made with your selected student. In the example, bcsxx represents your account name.
Message from Talk_Daemon@ribozyme at 19:19 ... talk: connection requested by bcsxx@ribozyme.vadms.wsu.edu. talk: respond with: talk bcsxx@ribozyme.vadms.wsu.edu
The screen clears and puts a [Waiting for your party to respond] statement on the top of the screen and a divider across the middle of the screen. It is now up to the student you are attempting to contact to make connection with you. The computer will tell you with a [Connection established] statement. If he or she is slow to respond to your call, you will see the following message, [Ringing your party again]. Now introduce yourselves and have a short chat, maybe about the weather. When one of you has had enough of this chat, enter the term bye and press the control and c keys together. A [Connections closing. Exiting] message will appear and you will be returned to the machine prompt.
At times when you can't reach another person who is on the machine, you can use electronic mail. On ribozyme, electronic mail is handled by the program, pine. Pine allows you to send and receive electronic mail from other users on this machine as well as from all other computer users that know that you have an account on this machine.
This function is activated by entering the term, pine.
% pine
The following screen comes up on your terminal. The beginning screen has the FOLDER LIST line highlighted. The program will tell you how many messages are waiting for you. This mailing program doesn't distinguish between new, unread mail and old saved messages in the INBOX portion of your mail folder. If you want to have this message really mean something, get in the practice of reading and moving mail out of the INBOX each time you receive a new piece of electronic mail.
PINE 3.91 MAIN MENU Folder: INBOX 0 Messages
? HELP - Get help using Pine
C COMPOSE MESSAGE - Compose and send a message
I FOLDER INDEX - View messages in current folder
L FOLDER LIST - Select a folder to view
A ADDRESS BOOK - Update address book
S SETUP - Configure or update Pine
Q QUIT - Exit the Pine program
Copyright 1989-1996. PINE is a trademark of the University of Washington.
[Folder "INBOX" opened with 0 messages]
? Help P PrevCmd R RelNotes
O OTHER CMDS L [ListFldrs] N NextCmd K KBLock
To send a message, either move the cursor with the arrow keys up to the Compose Message line or press the c key. Once in compose mode, the following screen appears on the screen (this is a reduced version of the actual image on your terminal). Now send a message to the teacher account telling your instructors about your computing experiences so far. Include information in your note about who you are, what the complete path to your home directory is, the size of your .login file, and tell about your talk session. You will start your message by entering teacher in the To: line. Pressing the RETURN key causes the term teacher to change to Instructional account <teacher@ribozyme.vadms.wsu.edu> and moves you down to the next line. Just press the RETURN key again until you are down on the Subject: line. On this line enter the term, contact. After pressing the RETURN key, you are ready to enter your message.
PINE 3.91 COMPOSE MESSAGE Folder: INBOX 0 Messages To :teacher Cc : Attchmnt: Subject : ----- Message Text ----- /////////////// empty space until the bottom of the screen /////////////// ^G Get Help ^X Send ^R Rich Hdr ^Y PrvPg/Top ^K Cut Line ^O Postpone ^C Cancel ^D Del Char ^J Attach ^V NxtPg/End ^U UnDel Line^T To AddrBk
The pine program uses the pico editor for creating its messages. You will be using pico to do additional editing later in this exercise. When your message is complete, press the Ctrl and x keys at the same time to send it off. The help section at the bottom of the screen uses a ^ symbol to denote the Ctrl key. The following lines appear at the bottom of the screen. Enter y to send the message.
Send message ?
Y [Yes]
^C Cancel N No
A quick line containing Writing Fcc flashes on the screen. Then the following line, [Message sent and copied to "sent-mail".], appears on the screen. You are returned to the main menu. At this point to exit the program you can enter q, or use the arrow keys to move the highlighted line down to the Quit line and press the RETURN key. At the bottom of the screen, the following line appears and you are returned to the machine prompt. After you have been in the pine mailer a new file will appear in your account, .pine-debugx. There will be a maximum of four of these files and they are due to the way the mailer was installed on the system. There are other files that are pine related. These are .addressbook, .addressbook.lu and .pinerc. Do not delete these files. They are required by the pine program.
Pine finished -- Closed empty folder "INBOX"
There is more information about the pine mailer in the carrel. Additional information on the program is in the Using the Pine Mailer handout.
This section explores communications with the outside world via the computer networks, the Internet network in particular. Many colleges and universities across the world are linked to one another via the Internet network. Access to this network is free and meant to assist the flow of research information.
For the purpose of this section, assume the following data:
l) You are working in a lab where the advisor is computer-aware, but doesn't really use computers. Needless to say computer operations have fallen on your shoulders.
2) Your boss, Dr. E. L. Slow, has just returned from a European conference where he met an individual from Sweden who is on sabbatical in the U.S., with whom he plans to collaborate with on his favorite project, snake toxins. He has brought back notes on how to contact his new colleague, Dr. Mats Sundvall of Uppsala University. Dr. Sundvall will share the username of the individual he is working with here in the U.S. Slow wants you to contact Dr. Sundvall and get the new snake toxin sequence he has been working on.
3) You have contacted the ribozyme system manager and now have the following piece of information:
Using the above information, send a request to Dr. Sundvall, who regularly reads his e-mail, for the desired snake toxin sequence. When the sequence is returned to you via an e-mail message, let your boss, who uses the ribozyme account teacher, know that it has arrived. Please remember that Dr. Sundvall doesn't know who you are, or that you work for Dr. Slow, so be polite and formally request the information from him giving appropriate background information. Use the information given in the previous section to help you with this task.
Software programs are not normally written in UNIX script, they are written in standard programming languages such as FORTRAN, PASCAL or C. Programs may be complex, requiring users to be extremely knowledgeable.
One program that is extremely easy to use and requires no user input other than typing its name isContact. Not all software is this easy to use, but well-written software should explain what it does, query the user for necessary information and produce understandable output. Run the Contact program.
% contact
On the screen is the date and a comment on the difficulty of running the program. Most software is more meaningful, however you have just run a FORTRAN program on ribozyme.
Effective computer usage depends on your understanding of how the machine works and the development of editing skills. These skills allow you to gauge the nature of the tasks being done and determine how to most efficiently achieve them, take advantage of the more complex features of the computer's operating system, customize your working environment, write text files, and get access to batch processing.
Computers, such as ribozyme, operate most effectively when they are running computing tasks. Usage by normal users in interactive sessions (one where programs or tasks are being run directly from the keyboard) account for less than a third of the possible time that a machine is in service on a given day. Other computing processes require little, if any, user interactions, but consume a great deal of CPU time calculating complex numerical problems. The batch queue system was developed to even out the computing day load levels and provide for the needs of both interactive-intensive and calculation-intensive users.
Batch queues operate on a first come, first served basis. Queues operate at a lower priority level than interactive users and so run in the background during the day and take over the CPU during off operating hours.
Determining when a task should be sent to a batch queue or run interactively depends on user experience with the software being used. Software manuals often tell whether a program can be run in batch mode or not. Some programs work on small data sets easily in interactive mode, but should be run in batch mode when large data sets are used. Older computer software for doing computational work was all written to be run as batch jobs.
To do batch processing, you must be able to create and edit text files. This requires learning how to use the editor on ribozyme, the pico program. Using pico in this class is complicated by the fact that an emulator is being used to make contact with the computer.
Necessary Editing Functions
In the following section the ^ symbol denotes the control key from the keyboard. This is the same convention used by the pico editing program in its documentation.
Moving through Text
There are three ways to move through text:
1) The use of arrow keys allows line by line movement through a file. This procedure is not bad for small files with few lines of text.
2) In pico, move by about 19 lines of text down through the file by using the ^v keys on the clone keyboard This means of movement is useful for medium-sized files. To move in the reverse direction enter ^y.
3) Move by using the find function of the pico program, ^w. A prompt will request a phrase to be located (search [term] : ). Enter the desired phrase and press the RETURN key. If the desired phrase is in the text, the screen will show that portion of the text in which it appears and the cursor will be positioned on the start of that phrase. Otherwise the program will state that the phrase cannot be found by putting a message at the bottom of the screen. This process is useful when dealing with large files, providing distinctive terms can be found to allow movement to the desired locations.
Selecting Text
Selecting text makes the movement of text from one location to another easier and also allows you to delete text.
1) Find the phrase to be selected.
2) Move the cursor over to that phrase.
3) Press the Ctrl, shift, and 6 keys all at the same time. This will activate the selection process and a message will appear at the bottom of the screen stating [Mark Set]. Now either move the cursor to the right or left for an individual word or a short phrase, or up and down the screen for blocks of text with the arrow keys. Once the entire section to be selected has been highlighted, press ^k to remove it from the screen and put it into a buffer. What you want to do with this text (removal, copying or moving) determines what step is taken next. (See later sections on removing text and inserting text for details on these procedures.)
Removing text
You can remove either a single character, a word or blocks of text. There are two ways to remove text:
1) Use the delete key. Position the cursor to the right of the character to be removed. Press the delete key as many times as needed to remove the unwanted text from the screen and the file.
2) Use the selecting text procedure in pico. By not inserting whatever text was stored in the buffer and/or placing new information into the buffer, the original text is lost.
Inserting Text
There are two ways to insert text into a file:
1) Move the cursor to the desired spot in the text and simply begin to type in the new text.
2) If text is to be moved from another section of the file or copied from somewhere else in the text to a new spot, then use the select text procedure to place the desired section of text into the buffer. To copy the text into the buffer, press ^k, and then ^u to restore the text to its original site. Then move to the new site and press ^u again to copy the text into its new location. For moving text from one site to another, just don't restore the text to its original location prior to moving over to the new one.
6) Using the Editor, Pico
Editing on ribozyme is different than doing text editing with a personal computer. The pico editor is not as versatile as many of the simplest PC text editors. It is mainly a straight ascii editor with no special fonts or highlighting possible. This is due to the nature of the terminals it is used with. Accept these limitations and don't plan to use it to produce items for publication. It is still a good editor with usable features. A copy of the pico help file is included at the end of this exercise for reference.
Editing is a necessary skill to have on a computer regardless of the software you use. By being able to create text files, you can more effectively control computing activities, use a greater variety of software, modify output files and communicate with others.
To activate this utility, enter the term pico followed by the name of the file to be worked on. Use the filename change.txt for this first use of pico.
% pico change.txt
Since the file didn't exist before, you will get the message at the bottom of the screen stating [New File].
The cursor will flash at the top of an empty screen awaiting the entry of text. Just start entering your text. Make this a note to anyone you please. Refer back to the editing information in the previous section of this week's exercise for assistance in the various aspects of editing, such as moving blocks of text, deleting characters, etc. When finished with the note, press ^x. The program will prompt you about saving the modified buffer, respond by entering y. Pico will check with you about the name of the file. If you still want to keep the name listed there, just press the RETURN key and the file will be saved under the filename change.txt.
Look at your newly created text file by typing it off on the screen. This is a good way to check for errors that weren't obvious when creating the file.
% cat change.txt
Now revise the file, insert additional text, correct spelling mistakes, whatever. Pico reacts differently with a file that already exists compared to one that didn't. This time it will tell you the number of lines contained in the change.txt file at the bottom of the screen.
% pico change.txt
The cursor will be on the first line of your text waiting to be moved throughout the text to make modifications.
Use the cursor control keys or global movement keys to move through the text, and change it as you need or just enter more text. You will exit the program by the procedure given previously when you first edited the change.txt file. Not saving the modified buffer will leave the file as it was originally just in case you want to abort a disastrous editing session.
Editing is a very important part of being able to effectively do computing tasks. Therefore, some more practice with the technique is called for. This time you will edit an existing file and provide information about yourself and your level of computing skills. Just enter the data and put x's to denote your experience with various types of computing tasks or operating systems.
% pico bc578q.txt
Since the next step is to send off this file to the teacher account, and everyone else in the course has the same file with the same name in their accounts, rename the bc578q.txt file to reflect your name by entering a command line similar to that given below, where (your lastname) is your last name.
% cp bc578q.txt (your lastname).txt
Now send off the file using the following command line. The (your lastname).txt represents the name of your file.
% rcp (your lastname).txt teacher@ribozyme:receive
Now fill out another existing file. This one will be to be used later by your instructors in helping you with your project.
% pico bc5781.txt
Rename the bc5781.txt file to reflect your name by entering a command line similar to that given below, where (your lastname) is your last name.
% cp bc5781.txt (your lastname).txt
Send the file using the following command line. The (your lastname).txt represents the name of your second edited file.
% rcp (your lastname).txt teacher@ribozyme:receive
Yet more practice is needed to really acquire this vital computing skill. Therefore, copy over the three files starting with p in the $GRAD_DIR/week2 location into your account and use them to become an effective file manipulator. Each of these three new files contains instructions at the top of the file telling you how to work with the data contained therein. Do a ls -la to determine the names of the files and then use pico to make the desired changes.
% cp $GRAD_DIR/week2/p*.* .
% ls -la p*
Record the names of the files that start with p.
__________________________________________________________________
__________________________________________________________________
Use the following example command line to edit the first of these files. Here
pxxxxx1.txt represents the name of the first file.
% pico pxxxxx1.txt
When you have finished with each file, use cp to rename it (your lastname).txtX, where X is the number of the original file. Then use rcp to send it over to the teacher account. An example set of commands is given below using the first file in this set of practice files.
% cp practice1.txt (your lastname).txt1 % rcp (your lastname).txt1 teacher@ribozyme:receive
Computing is generally taken quite seriously. When you are just starting out using the computer everything is new and confusing. Relax and do something for fun. Enter the following command lines. The first one copies over a file, and the second one shows you its contents.
% cp $GRAD_DIR/data/humor.txt . % cat humor.txt
See, not all computing is meant to be taken seriously. After all there are games and bulletin boards on computers too.
Copy over a report form for this exercise, rename it to have your last name, go into the file and use the editor, pico to fill the report and send it to the teacher account.
% cp $GRAD_DIR/week2/week2.week2 . % cp week2.week2 (your lastname).week2 % pico (your lastname).week2 % rcp (your lastname).week2 teacher@ribozyme:receiveThis concludes your computing session for this week. Now log off of the computer by entering the command line given below.
% logout
You are no longer on ribozyme, but you are still in the emulator program. Use the arrow to move to the File location of the control bar. This is a pull-down menu. From this listing select the QUIT option to exit the session and release the mouse button. This moves you back to the Launcher window screen.
A copy of a pico help file and a Basic Unix for Beginners guide is included at the end of this exercise.
Pico Help Text
Pico is designed to be a simple, easy-to-use text editor with a
layout very similar to the pine mailer. The status line at the
top of the display shows pico's version, the current file being
edited and whether or not there are outstanding modifications
that have not been saved. The third line from the bottom is used
to report informational messages and for additional command input.
The bottom two lines list the available editing commands.
Each character typed is automatically inserted into the buffer
at the current cursor position. Editing commands and cursor
movement (besides arrow keys) are given to pico by typing
special control-key sequences. A caret, '^', is used to denote
the control key, sometimes marked "CTRL", so the CTRL-q key
combination is written as ^Q.
The following functions are available in pico (where applicable,
corresponding function key commands are in parentheses).
The following functions are available in pico (where applicable,
corresponding function key commands are in parentheses).
^G (F1) Display this help text.
^F move Forward a character.
^B move Backward a character.
^P move to the Previous line.
^N move to the Next line.
^A move to the beginning of the current line.
^E move to the End of the current line.
^V (F8) move forward a page of text.
^Y (F7) move backward a page of text.
^W (F6) Search for (where is) text, neglecting case.
^L Refresh the display.
^D Delete the character at the cursor position.
^^ Mark cursor position as beginning of selected text.
Note: Setting mark when already set unselects text.
^K (F9) Cut selected text (displayed in inverse characters).
Note: The selected text's boundary on the cursor side
ends at the left edge of the cursor. So, with
selected text to the left of the cursor, the
character under the cursor is not selected.
^U (F10) Uncut (paste) last cut text inserting it at the
current cursor position.
^I Insert a tab at the current cursor position.
^J (F4) Format (justify) the current paragraph.
Note: paragraphs delimited by blank lines or indentation.
^T (F12) To invoke the spelling checker
^C (F11) Report current cursor position
^R (F5) Insert an external file at the current cursor position.
^O (F3) Output the current buffer to a file, saving it.
^X (F2) Exit pico, saving buffer.
Pine and Pico are trademarks of the University of Washington.
No commercial use of these trademarks may be made without prior
written permission of the University of Washington.