Ubuntu Maverick for PhD Students

Please see the updated version of this article about installation of software for research in Ubuntu 12.04.

Some time ago I wrote a post about Ubuntu for PhD students, where I gave instructions on how to set up programs and libraries relevant for research on the Ubuntu linux distribution. This was for Ubuntu 8.10, so now I think it's time to update the information for Ubuntu 10.10 (codenamed "maverick"), a distribution which I can warmly recommend, by the way.

Software for research

What does research include? In short maybe this list comprehends some (not all) basic tasks involved: reading articles, doing statistics, illustration, writing articles.

I start by listing again some basic free software tools that I think are essential for research. My list cannot be inclusive and I leave out many more programs or libraries that I think are good but not as essential. Please feel free to suggest other programs in the comment section.

Connectivity

• The ssh server.
  
• Google Chromium (Chrome) - because it's very fast and now supports smart bookmarks (at least in linux versions)
  

Programming

• Powerful editors such as vim and emacs,
  
• gnu toolchain,
  
• gnu screen,
  
• subversion (svn), git,
  
• file converter from dos to unix (tofrodos),
  

Statistical tools

• GNU R,
  
• GNU octave,
  
• python with scipy,
  
• maxima,
  
• gnu scientific library.
  

Article writing and reference management

• texlive,
  
• many latex packages,
  
• jabref and bibutils for converting to and from other reference formats.
  

Illustration

• graphviz,
  
• ImageMagick,
  
• gnuplot, pdfedit,
  
• inkscape,
  
• Scribus,
  
• gimp,
  
• plugins to play media contents, etc.
  

Others

• perl,
  
• java RE and SDK,
  
• blas
  
• boost libraries
  

Installation

In the terminal, become superuser (sudo su).
For java, you'll have to do first include a new repository:
> add-apt-repository "deb http://archive.canonical.com/ maverick partner"
For chromium, we include the google repository:
> add-apt-repository "deb http://dl.google.com/linux/deb/ stable main"
> wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -

(If you don't have add-apt-repository installed, you can add the repository manually: echo "deb http://archive.canonical.com/ maverick partner" >> /etc/apt/sources.list)

We update package sources:
> apt-get update
Now let's get on it. Execute this and you will have plenty of time to grab some coffee.
> apt-get install openssh-server build-essential gcc gcc-doc apt-file gcj gsl-bin gsl-doc-pdf gsl-ref-html libgsl0-dev gsl-bin gsl-doc-pdf libgsl0-dbg libgsl0ldbl glibc-doc libblas-dev maxima maxima-share subversion subversion-tools git screen $(aptitude search R| grep -v ^i | awk '{print $2}' | grep ^r-) octave $(aptitude search texlive | grep -v ^i | awk '{print $2}') untex luatex latex-xft-fonts perl fontforge context-nonfree context-doc-nonfree dvipng imagemagick graphviz gnuplot-x11 gnuplot-doc gnuplot libatlas3gf-base kdevelop kate kile vim-gtk vim vim-addon-manager vim-common vim-doc vim-latexsuite latex2html latex-beamer xpdf writer2latex jabref bibutils hevea hevea-doc wordnet cups-pdf djvulibre-bin djvulibre-plugin pdfedit inkscape scribus pdf2djvu pdf2svg python2.6 ipython python3-dev python3-all python2.6-dev python-scipy unrar tofrodos epiphany-browser epiphany-extensions scribes lyx claws-mail claws-mail-i18n claws-mail-doc claws-mail-tools libqt4-core libqt4-gui flashplugin-nonfree ubuntu-restricted-extras regionset soundconverter gxine libxine1-ffmpeg libstdc++5 libmms0 google-chrome-stable
What I don't cover here is the installation of other programs such as Adobe Acrobat Reader, Skype, mp3 codecs, or samba, which you can click-install in the ubuntu software center (in the GNOME menu, usually at the top, under applications). Neither did I include useful Firefox plugins.
I recommend Mendeley for library management (you can find me there).
You might want to see other of my articles for more tips, such as (for a short selection) smart bookmarks for faster web searches, how to synchronize web browser bookmarks on different work stations, personalize the vim editor, set up a revision control repository, and automatically synchronize data.
You can also see the UbuntuScience community page for some additional information.
Enjoy. Please leave more suggestions below.