Department Computing Operations

• Frequently Asked Questions (FAQ)
• Linux Workshops
• Department File Format Policies
• StatCompServerInfo
• Computing Clinic
• Planned Changes to Biostatistics twiki
• Overview of Biostatistics IT Services

Data Transmission

• The Data-Hippo Secure Data Transfer Application
• DataDeposit

Linux Workstation Setup

• User workstation setup and configuration
  • Old sylpheed instructions
• Recommended directory and e-mail folder organization
• Instructions to vendor for workstation configuration
• How to create system scripts
• NotesOnUdev
• MappingBiostatShares
• MappingVanderbiltShares

Database Project

• Database specification
• Research Database Goals

Webcalendar

• WebCalendar instructions and help

Twiki

• Hints and help for using and editing the Twiki
• A template for the user page
• Twiki Access Discussion
• HtmlToTwiki

CVS

• Information on the Biostat CVS Server
• CVSWeb -- Browse the Biostat CVS Server

Common Text Editors

Information about common editors and IDEs

• KDE editors: Kate, Kwrite
• Emacs
• Vi/Vim
• Eclipse

Exim (debian mail setup)

• Run the following commands
  • cd /etc/exim4/
  • update-exim4.conf -o ./exim4.conf
• Edit /etc/aliases and remove the line "root: staff"
• Edit /etc/inetd.conf and add the following line:
  smtp            stream  tcp     nowait  mail    /usr/sbin/exim4 exim4 -bs
• Restart inetd by running /etc/init.d/inetd restart
• Make sure exim works by running something like:
  exim4 -v vunetid@localhost.localdomain
To: vunetid@localhost.localdomain
From: someguy@someplace.com
Subject: testing exim4
Testing!
.
• then run "mail" to see if you have mail. If you do, you're done!

RSPerl

• RSPerl is an R module that works with Perl. With it you can run R commands inside Perl and vice versa. Below are the instructions to get the Perl module working (so you can run R from Perl scripts).
• Note: you must recompile R from the source, since RSPerl requires R's shared library. Below are instructions on how to do this.
  • make a directory in your home folder for the R source file (ex: /home/vunetid/src) by running "mkdir /home/vunetid/src"
  • change your current directory to the one you just created
  • download the R source files by running "wget http://www.biometrics.mtu.edu/CRAN/src/base/R-2/R-2.1.1.tar.gz" or by grabbing them from a mirror on the R website
  • unzip the tarball by running "tar -xvzf R-2.1.1.tar.gz"
  • cd into the R directory ("cd R-2.1.1")
  • run: CFLAGS="-g" CXXFLAGS="-g" FFLAGS="-g" ./configure --enable-R-shlib
  • then run "make" (but don't run "make install", this will leave the R files in your home directory)
  • now it's time to install RSPerl
• Download the source code (RSPerl_x.x-x.tar.gz) from the RSPerl website.
• Install by running "R CMD INSTALL -c -l /home/vunetid/src/R-2.1.1/library --configure-args='--with-in-perl' RSPerl_x.x-x.tar.gz"
• Edit your ~/.bashrc file and add the following lines:
  • export R_LIBS="/home/vunetid/src/R-2.1.1/library/"
  • export PATH="/home/vunetid/src/R-2.1.1/bin:$PATH"
  • export PERLLIB="/home/vunetid/src/R-2.1.1/library/RSPerl/share/blib/arch:/home/vunetid/src/R-2.1.1/library/RSPerl/share/blib/lib:/home/vunetid/src/R-2.1.1/library/RSPerl/scripts"
  • export LD_LIBRARY_PATH="/home/vunetid/src/R-2.1.1/bin:/home/vunetid/src/R-2.1.1/lib"
  • export R_HOME="/home/vunetid/src/R-2.1.1"
• Reload your .bashrc by running "source ~/.bashrc"
• Test to make sure your installation was successful by running "perl ~/src/R-2.1.1/library/RSPerl/scripts/test.pl"
• If you have any questions, please ask JeremyStephens. Good luck!

System Imager

• Using SystemImager to provide our own system images

Viewing and Changing PDF Documents

• Recommended PDF readers: okular, kpdf, xpdf (not fancy but extremely fast), acroread, gpdf
• Annotating PDF documents
• Manipulating PDF documents

Printing

• Instructions for setting up access to the Xerox Phaser 6250 DP color laser printer
• Various CUPS Knowlege

Linux

• Various Linux Errors & Solutions
• Installing extra languages for KDE
• Linux related web links (distribution ISOs, apt repository, etc)
• Improving User Efficiency
• User Survey Draft
• Konqueror Web Shortcuts, for web browsing
• Nashville Linux Users Group

LaTex Links and Notes | See also DocProcess

• LaTex cheat sheet
• a nice LaTex help page from someone at NASA
• Problems with updating LaTeX (tetex-bin)

The tetex-bin debian file can sometimes be difficult to update. Part of the reason are "ls-R" files that contain various path information. They are in such places as "/var/cache/fonts", "/var/lib/texmf", and "/usr/share/texmf". Try deleting these files and running either mktexlsr or texhash in those directories. Then reconfigure tetex-bin with the command dpkg-reconfigure tetex-bin.

• Commands to invoke LaTex and view or print the output:

      Linux
      $ latex test.tex   # invokes LaTex, processes test.tex, and writes test.dvi
      $ kdvi test.dvi    # opens test.dvi for viewing and printing
  
      Windows (MiKTex)
      > latex test.tex
      > yap test.tex
      

Todo

• Current IT Tasks