Introduction to Computing at UF Statistics
Intended audience
The audience for this document is the new graduate student or faculty
member in Statistics. It is assumed you have been using Microsoft
Windows to send email, browse the web, and write papers at this or
another University for the last several years, and you want to know
what additional software and services the Statistics department and UF
have to offer. It is also assumed you do not have hands-on experience
with Linux, and you wonder why we use it instead of Windows.
Phishing
Is this email real, or is it attempted fraud? How can you tell?
Hover your mouse over the link and look on the bottom line:
Does that URL point to somewhere authentic-looking within UF? Who is
"megabyet.net"?
And how about this one:
Hover your mouse over the link and look on the bottom line. Does that
URL point to Citibank?
If you get what seems to be a surprise email from your bank, TELEPHONE
your bank to ask about it! Use a phone number you already trust, such
as the phone number on the back of your ATM card or credit card.
Attitudes and techniques for not biting on a phishing hook
More techniques:
Current active recognized phishes on campus:
You gave out your financial info to a phisher, now what?
Central computing groups on campus
For those of you new to UF, I want to mention a few of the other large
central computing groups on campus before I talk about Statistics
resources. Some of these you will be working with daily, and some you
may never directly talk to. All of them are important.
Academic Technology (AT; formerly OIR, CIRCA)
The group whose name was formerly CIRCA (Center for Instructional,
Research, and Computing Activities) merged with the group whose name
was formerly OIR (Office of Instructional Resources), to form the
group named AT (Academic Technology). Currently they run several
Windows-based computing labs, the undergraduate computing helpdesk,
the Gatorlink helpdesk, the first-level PeopleSoft helpdesk, and a
bunch of other things. If you are new to UF you will need to visit
them on the 5th floor of the CSE (Computer Science and Engineering)
building to receive a Gatorlink identification card. You should do
this in your first week. You have already received your Gatorlink
account in the process of spplying to UF.
Computing and Network Services (CNS; formerly NERDC)
The group whose name was formerly NERDC (Northeast Regional Data
Center) has been renamed CNS (Computing and Network Services). They
maintain the network plumbing that brings the Internet to every
building, shed, and doghouse on campus, and run Gatorlink mail and
dialup. They probe every Windows machine they can find for viruses
from time to time, and this includes personal laptops attached by
wireless. You may never interact with them directly unless your
personal Windows machine contracts a particularly malevolent virus.
Bridges / Peoplesoft (formerly ERP)
The group whose name was formerly ERP (Enterprise Resource Planning)
and is now named Bridges, runs the ERP software named PeopleSoft on
several IBM Unix mainframes. Currently PeopleSoft has replaced the
financial functions of general ledger and payroll that were formerly
distributed between the CNS mainframe and the State of Florida
mainframe. It appears like the registrar function will remain on the
IBM CICS mainframe. You will be interacting with PeopleSoft for time
reporting for some appointments.
Central computing services on campus
Gatorlink Email
Gatorlink email is a web-based email service with about 50,000 users.
Repeated unreasonable blacklisting of Gatorlink by AOL for a small
percentage of spam has caused the University to ask that your UF email
address of record, the one listed in directory.ufl.edu, not be
forwarded off-campus. Gatorlink is a legitimate final destination.
Wireless
There is wireless service inside of Griffin-Floyd, and all over
campus. The general access ones are all named “uf”, just
connect to the one with the highest signal strength. Open a browser
and read any web page. You will be redirected to a login screen that
accepts your Gatorlink to activate the port. Make sure you know the
name of the wireless you're trying to use. If you're inside
Griffin-Floyd, you may receive the uf wireless from the plaza next
door, which has too low of a signal to be reliable, or the Chemistry
one named Chemnet, which you don't have logins for.
Walk-up Internet ports
There are some ethernet ports, mostly in AT lab spaces, that are
available for campus community use. Plug in and open a browser the
same way as wireless.
Personal laptops, viruses, and network connections
In the past, we've found that 5 of the 25 laptops newly introduced to
the Statistics network in a year were caught breaking into other
machines within a week, even after passing an initial virus scan.
Therefore, personal laptops may now only be connected via the wireless
service, which is better equipped to identify and isolate infections.
The McAfee virus scanner is site-licensed to UF for both school and
home use. If you receive a paycheck from UF, you are also site
licensed to use any version of Windows and any version of MS Office.
If you are using old versions, please don't hesitate to upgrade to a
newer version that receives more comprehensive security patches. The
McAfee is available through http://software.ufl.edu, and you
can purchase media for Windows and Office versions at the bookstore in
the Reitz Union.
Email
Your email address is yourlogin@stat.ufl.edu, and that is
where official departmental notices will be sent. We don't mind if
you forward your email elsewhere, as long as you read it! All
incoming messages are eventually accepted, but messages deemed to be
spam are filtered into the folders Spam, Virus, or Banned. Messages
in these folders older than two weeks are automatically deleted. You
can ignore these folders until you think you may be missing something.
We believe we get extremely few false positives on our spam filtering.
You can access your Statistics department mail several ways. The
majority of Statistics users read their mail through Thunderbird,
either from the lab or office systems, their own laptop, or their own
machine at home. Users on the road often read their mail through
http://webmail.stat.ufl.edu.
Instructions to set up your own Thunderbird or Mozilla to interact
with our mail server are at
http://www.stat.ufl.edu/system/imap.bb.shtml.
Personal web page
Instructions for setting up a personal web page are at
http://www.stat.ufl.edu/system/homepage.shtml
One problem that comes up occasionally with TAs is that for privacy
reasons you must never publish Social Security numbers or UFID numbers
on the web. I know it's convenient to return test results that way,
but you must not do it.
How is Linux different from Windows
At the moment you're probably using Windows, and it works for you, so
what's the big deal with Linux? Below are some computing concepts
which you probably haven't been exposed to in the Windows world. My
goal is to expand and improve your computer experience.
Reliability and security
For practical purposes, Linux never catches viruses, and doesn't spend
most of its lifetime being twitchy and slow. Once Linux is customized
to the the quirks of particular hardware, it will run well on it
indefinitely. You don't need to reload Linux every six months to get
your performance back. Also, it is common to stay logged into a Linux
machine for months at a time. This is a “desktop”
experience much like a physical desk. You can interrupt work in
progress and expect to be able to go back to it later. The sight of
the arrangement you left it in will jog your memory of what you were
doing. If you're doing this on a laptop, your suspend and restore
feature must be rock solid.
On all the time
Linux is on all the time, and as long as it's on, it may as well be
doing work for you. What sort of computations could you do with 35
machines that are on all the time? Linux is multiuser, so your use of
a machine doesn't prevent anyone else from using it, as long as you
exercise good taste about resource consumption.
Easy programming: the shell
Windows generally has exactly one way to control a program: the GUI
(Graphical User Interface). By contrast, Linux usually has one, the
shell command line, and occasionally a second, a GUI. For instance,
the shell command wget can copy an entire web tree in a
single operation, which is complimentary to the interactive work you
can do in a browser. Linux programs are designed as Lego building
blocks that you snap together. Programming Linux starts off easy,
with scripting. You put a couple commands with long arguments in a
file, so you don't have to keep typing them in. Perhaps these
commands sync portions of your laptop disk to your Statistics account
for backup purposes. Then you add a couple more commands, perhaps to
keep dated backup versions. Soon you're outside of the range of what
you could achieve on Windows. The shell is what lets you plug
together 2,400 little building-block programs. You will soon know the
names of 50 of them corresponding to things like dir and
copy from Windows, and every program you can use as a
“command” is one you can script. The Linux statistical
computing environments, such as R, leverage rather than attempt to
replace these tools.
Feature stability
I have been using essentially the same editor (emacs) and email
program (mh-e) for 20 years. That's before the web, and five years
before Microsoft Windows 3.0. Imagine the payback on my investment in
learning those programs. How many different Windows editors and email
programs have you had to learn in that time?
X-Windows remote display
Linux has the concept that where you run a program can be different
from where you interact with the program. You can run your big
crunchy R program on the meaty server on the closet, but you don't
have to physically sit in the closet in front of the console.
Instead, you can send the GUI back to your desk.
Mathematical typesetting
The world standard for mathematical typesetting is the TeX (pronounced
“tech”, spelled “tex”) family of programs. Of
these the frontrunner is LaTeX (pronounced “la-tech”,
spelled “latex”). With improvements to latex in the last
decade you are not limited to the classic latex style. Like HTML,
Latex is an example of the “markup” style of typesetting
systems. In a markup system, the text of the document is interspersed
with declarations about what purposes the pieces of text serve in the
document, and to a lesser extent what the text should look like.
Latex has been improved and simplified quite a bit in the last decade.
There's a whole lot of latex code floating around that is more
cumbersome than it needs to be now, so latex is an exception to the
general rule of programming that you should learn by copying code from
other programs. Save yourself hassle and write your latex from
scratch with a good reference book like Kopka. However, there is
dedicated University support for writing your thesis in latex, which
you should not do from scratch. Ask others when you are ready.
Word Processing
Word processing for small things with no mathematics like a letter to
a potential employer can be done perfectly well in latex. However, if
you're doing something that's mostly graphics design like a sign, you
might find one of the Adobe Illustrator or Visio clones a better match
for the problem. Try out inkscape, dia,
and xfig. For the Adobe Photoshop kind of bitmap editing,
use gimp. If you're graphing data, use R.
Latex example
A letter on the departmental letterhead looks like this:
\documentclass[12pt]{letter}
\usepackage{epsf}
\usepackage{myltr}
\usepackage{times}
\begin{document}
\date{August 19, 2010}
\signature{My Name}
\address{}
\begin{letter}{}
\opening{Dear Mom,}
Word processing in Latex was easier than I had feared. Now I can do
all of my professional work in latex on Linux!
\closing{Love,}
\end{letter}
\end{document}
This letter depends on the file myltr.sty, wherein I have customized
my name and address into the letterhead. However, if you remove the
usepackage for myltr, it will work standalone, sans letterhead.
Microsoft Office compatibility
Microsoft Office files can be read by Open Office. As of August 2010,
Open Office's compatibility is good enough to read Office documents,
but not good enough to reliably collaborate with Office users. The
shell command to start up the Open Office suite is ooffice,
or oocalc, oodraw, oowriter, and
ooimpress (PowerPoint clone) for the individual pieces.
Statistical Software
R
R is a free software clone of S. It has collected lots of free
software development interest. It is a serious program which is
attracting careers of professional work. We recommend it due to the
open source benefits of longevity and control. It runs nicely inside
emacs. If you implement your statistical research results in R and
publicize them, it is much more likely that people will use them.
Example of R
The shell command is R. A session looks like this:
bb@mako:~$ R
R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> x <- rnorm(50)
> y <- 2*x+rnorm(50, sd=0.4)
> plot(x,y)
> q()
Save workspace image? [y/n/c]: n
bb@mako:~$
After the plot command, a window appears showing the plot. The
“Save workspace image?” question wants to save all the
variables and functions you've created within R's memory into a file,
so that you can read them all back in and pick up where you left off
in a later R session. Most R users I've spoken to tend not to use
saved environments, instead preferring to keep their data and
functions in ordinary text files where they can “put their hands
on them”.
Specific commands
Windows equivalents
| Windows | Unix |
| dir | ls |
| cd | cd |
| copy | cp |
| rename | mv |
| del | rm |
| pwd | pwd |
| more | more |
| print | lpr |
| help | man |
File viewers
| PDF | xpdf, acroread |
| PostScript | gv |
| GIF, JPEG | xloadimage, gimp |
(C) University of Florida, Gainesville, FL 32611; (352) 392-1941.
This page was last updated Tue Sep 25 01:14:34 EDT 2012 |
 |
