Summary: This laboratory reviews some mechanics
related to the use of the Computer Science Linux Network for
Bioinformatics.
Specifically, this lab gives you the opportunity to explore:
-
Logging In
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The Linux/Gnome Window Environment
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Practice with a Terminal Window: Changing Your Password
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Iceweasel/Firefox
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Python
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Finishing Up and Logging Out
Please don't be intimidated! Although this lab
contains many details which may seem overwhelming at first, these
mechanics will become familiar rather quickly. Feel free to talk to
the instructor or with a Linux User Consultant if you have questions
or want additional help!
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On the computer in front of you, you should see a small window that asks
you to log in. If you don't see such a window, try hitting a key on the
keyboard or clicking the power button on the monitor.
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Enter your user name. Press the Enter key.
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Enter your password (which won't appear). Press the
Enter key.
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Get help if those previous two steps don't work.
To use any of the computers on Grinnell's Linux network, one must
log in, identifying oneself by giving a
user name
and a password. You will have received a Linux
user name and password from the instructor if you did not already
have one. If you have not received a Linux user name and password,
or if you have forgotten either one, please tell your instructor.
When a Linux workstation is not in use, it will display
a login screen with a space into which one
can type one's user name and, later, one's password. (If the
workstation's monitor is dark, move the mouse
a bit and the login screen will appear.) To begin, move the mouse
onto any part of the box containing the login box. Type in your user
name, in lower-case letters, and press the Enter key.
The login screen will be redrawn to acknowledge your user name and
to ask for your password; type it into the space provided and press
Enter. (Because no one else should see your password,
it is not displayed on screen as you type it in.)
At this point, a computer program that is running on the workstation
consults a table of valid user names and passwords. If it does not
find the particular combination that you have supplied, it prints
a brief message saying that the attempt to log in was unsuccessful
and then returns to the login screen -- inviting you to try again.
Consult the instructor or the system administrator if your attempts
to log in are still unsuccessful.
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You'll see something that looks somewhat like Microsoft Windows, but also
somewhat different.
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Icons at the bottom of the screen can be used to start programs.
Once you have logged in, a control panel will
appear at the bottom of the screen. Some other windows also may be
visible in other parts of your screen. All of these areas are managed
by a special program, called a windowing system.
On our network, login chores and other administrivia are handled by a
program or operating system, called Linux, and the
primary user interaction is handled by a windowing system, called Gnome.
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Click on the picture of the small computer monitor in the taskbar. A new
window, called the Terminal, will appear.
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Type yppasswd and hit the Enter key
to change your password. You will
be prompted for your old password and your new password. (The letters
you type will not appear.)
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Type exit and then hit the Enter key
to close the window.
While we can run several programs directly, we will need to invoke
others by name. The computer program that reads and responds to
such invocations is called the shell, and
your interactions with the shell takes place in a window generated
by a program called a terminal emulator, or
terminal for short.
You may already have a Terminal window on screen.
If not, you can start one at any time by moving the pointer onto the
small monitor icon at the bottom middle of the front panel, and clicking
with the left mouse button. Shortly a window appears, displaying the
shell prompt -- the name of the workstation on
which the shell is running, followed by a percentage sign. This prompt
indicates that the shell is ready to receive instructions.
You type in such instructions using the keyboard. Move the mouse pointer
into the Terminal window and click the left mouse button to make
the window active. Notice that the window frame changes color following
the click, indicating that the window has become active.
To get rid of the Terminal window, press
Ctrl/D. That is, hold down either of the keys marked
Ctrl, just below the Shift keys, and
simultaneously press the D key. (On our
workstations' keyboards, the keys marked Ctrl
(control
) and Alt (alt
or meta
) are somewhat like
Shift keys, in the sense that they modify the effect
of other keys that are pressed simultaneously.) The shell program
interprets Ctrl/D as a signal that you have no more
instructions for it and halts, and the terminal emulator closes the
window automatically once the shell stops running. Alternatively, you
may close a window by moving the mouse to the x
at the top-right of the window, and clicking the left mouse button.
Finally, you can usually type exit to close a
terminal window.
It is a good idea to change the password associated with your account
shortly after you receive it and every few months thereafter. The program
that one uses to change one's password is by its name,
yppasswd
.
Choose a new password. Make it something that you can easily remember, but
not an English word or a name, since it is easy for system crackers to
break in by guessing your password if you choose it from one of those
categories.
Open a terminal window, select the window by clicking the left
mouse button in it, and type the word yppasswd. The
password program prompts you once for your old password -- the one
you logged in with -- and twice for your new password. Note that
nothing will appear when you type your password. To ensure that no
one eavesdrops on your password (or even the length of your password),
the workstation leaves the cursor in place while you are typing passwords.
If you give your old password correctly and the two copies of your
new password match, the program substitutes the new password for
the old one in the table that the login program consults. The old
password is discarded and will not be recognized in subsequent logins.
(If the attempt to change the password fails for any reason, however,
the old password is retained.)
A typical interaction to successfully change a password looks like this:
bourbaki% yppasswd
Changing NIS account information for user on jacobi.math.grin.edu.
Please enter old password:
Changing NIS password for user on jacobi.math.grin.edu.
Please enter new password:
Please retype new password:
The NIS password has been changed on jacobi.math.grin.edu.
bourbaki%
After running the yppasswd program, the shell
takes over again and issues another prompt. You can invoke as
many programs as you like from the shell, one after another, before
pressing Ctrl/D or exit to
leave the shell.
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Start Iceweasel by clicking on the picture of the small white creature
grasping a purple sphere.
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Agree to any dialog boxes that appear. They shouldn't appear again.
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Learn how to get to the front door for this class.
While some materials for this course will be available in paper, almost
everything for this course (including electronic versions of paper
materials) will be available on the World Wide Web. In this class, we
use a version of the Firefox browser called Iceweasel. Almost all of
the materials for this course will be distributed over the Web. To use
Iceweasel to view materials, such as this course's syllabus and this lab,
you may follow these steps:
First, prepare to use the World Wide Web by clicking on
the Iceweasel icon (the picture with small white creature
holding a green sphere). Iceweasel is a version of Mozilla
Firefox renamed to accommodate trademark issues. More info
on the relationship between Firefox and Iceweasel can be found at
http://en.wikipedia.org/wiki/Naming_conflict_between_Debian_and_Mozilla.
We will generally use the names interchangeably.
The first time you run Iceweasel on our network, two message boxes
might appear.
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One box might ask you to consent to the terms of a licensing agreement.
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One box might request permission to create some configuration files in
your home directory.
You should approve of any requests by clicking on the appropriate
word. The pop-up boxes then disappear; you should not see them on subsequent
uses of Iceweasel.
Initially, Iceweasel displays a World Wide Web document
containing some default information. You should switch to the
page http://www.cs.grinnell.edu/zero-one.xhtml,
which is an entry point to the Computer Science Department's Web site.
We expect that most of your are already familiar with a Web browser. If
not, please consult with one of us or with one of your colleagues.
To find material for this course, scroll down the origin
page for the Computer Science Department to the list of course
front doors. Now scroll down this page to find the entry for
this course, Bioinformatics,
and click on it to locate the front door
for this course. Next, click on the schedule
link to view the current draft of the semester's schedule.
You can also connect to the Web page for this class by selecting
Open Web Location from the
File
menu and then entering
http://www.cs.grinnell.edu/~rebelsky/Courses/CSC295/2009F/
Each Linux user can configure Iceweasel to reflect her or his
own preferences. Between logins, these preferences are stored in a file
in the user's home directory; when Iceweasel is started during a
later session, they are reinstated from that file.
Every user of Iceweasel in this class should establish a base page,
a starting point for browsing. Here are the Uniform Resource
Locators or URLs of some good choices:
To establish your base page, within Iceweasel, bring up the
Edit menu from the menu bar and select the
Preferences operation. A pop-up window
appears, allowing you to configure many features of the general
appearance of Iceweasel. Choose the General
option, if it has not been chosen already. The rectangle labeled
Home Page contains the URL of some document that
serves as the default. Replace the contents of this rectangle with
the URL of your choice. (This does not have to be a permanent change;
you can change your mind about this configuration at any time within
Iceweasel.)
To erase the current contents of the Home Page
Location(s) box, move the mouse pointer to the left of
the first character in the box, press the left mouse button and hold
it down, and drag the mouse pointer rightwards until the entire URL
is displayed in reverse video, white letters
on a black background. Then release the left mouse button and type
the new URL; the old one will vanish as soon as you start typing.
Once you have entered the new URL, move the mouse pointer onto the
button marked OK at the bottom of the pop-up
window and click on it with the left mouse button.
You can, of course, simply navigate to the page you want to use as your
home page and then click on Use Current Pages.
You may note that the button says Pages
(plural) rather
than Page
(singular). Since Iceweasel permits tabbed
browsing (that is, you can have tabs
within the same
window that you switch between), you can have a home set of tabs.
Particularly obsessive people might want to set up a sequence of tabs
with say, links to outlines, labs, readings, and beyond.
We're using Python as the programming language for this course,
and idle (the standard Python integrated development environment)
as the interface for idle.
Your first task in getting idle running correctly is to add an icon to
the task bar. (Almost as importantly, once you figure out how to add
an idle icon, you will also be able to add other applications that you
want to use.)
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Right click on the task bar. A pop-up menu should appear.
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Select Add to Panel ... from that menu.
A dialog box should appear.
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Select Custom Application Launcher,
which should be the first item in the dialog box, and then
click Add. Yet another dialog box should appear.
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Leave Type as Application.
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Enter "idle" in the Name field.
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Enter "/home/rebelsky/bin/idle" in the Command field.
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Enter "Python IDE" in the Comment field.
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Click OK
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Click Close to close the Add to Panel window.
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You should now see the new icon in your task bar. Try clicking it.
Most user interface systems provide a convenient way to access
commonly-used applications. In Gnome, we often add such applications
to the Task Bar. To add an application to the task bar, we need to
tell Gnome about where to find that application and what icon to
associate with the application. (We can tell it other things, too,
but that's enough for now.)
We will admit that we have not found an elegant way to automate the
addition of an icon to the panel, so you'll have to do it by hand. You
first tell the panel that you want to add something by right clicking
in an empty area of the panel and then selecting Add
to Panel .... (The ellipses tell you that you should
expect to provide more information.) We're going to add an application
launcher for a locally-developed application, so we must create a custom
application launcher. Click on the Custom Application
Launcher option and then click Add.
The Create Launcher window appears.
You will note that this window gives you about seven things to set up
for the launcher. The Name is what we use to refer to the application.
In this case, we'll use idle
. The launcher shows
this name when you pause the cursor over the icon for the application.
The Command is the most important thing to fill in. The command tells
the launcher how, in particular, to start your program. Typically,
we tell it where the program can be found and, in some cases,
provide additional information on how to launch it. You should enter
/home/rebelsky/bin/idle
(without the
quotation marks).
The Comment is additional information about the application, and also
appears when you pause the cursor over the icon for the application.
We suggest that you use Python IDE
here, but you can
choose other text that you find helpful.
You're almost done. You've chosen the name, command, and
description. You now need to click OK to accept the
new button, confirm that it appears, and then close the
Add to panel.
Now it's time to start idle. Click on the icon.
If you've successfully logged in, changed your password, started
Iceweasel, selected your base page, created an icon for idle
started idle, and played with multiple desktops, you've completed
the lab and you can finally stop. We're going to have you
log out (and then log back in again to do the next lab).
-
To log out, click on the menu icon near the lower left,
select Log out, and confirm.
-
Do not turn off the monitor or computers.
When you are done using a workstation, you must log
out in order to allow other people to use it. To log
out, move the pointer onto the menu icon near the left of the front
panel, click the left mouse button, and select the Log
out option. A confirmation box
will pop up, asking you to verify that you're ready to log out; move
the pointer onto the word Yes near the bottom
of this box and click the left mouse button. The Gnome windowing
system vanishes, and after a few seconds the login screen reappears;
this confirms that you're really logged out.
Please do not turn off the workstation when you are
finished. The Linux workstations are designed to operate continuously;
turning them off and on frequently actually shortens their life
expectancy.
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