Ubuntu Maverick for PhD Students


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

Meerkat. Image credit wikipedia: http://en.wikipedia.org/wiki/File:Meerkat_feb_09.jpgSome 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

Statistical tools

Article writing and reference management

Illustration

Others

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. 

3 Responses to "Ubuntu Maverick for PhD Students"

My contribution:
- Kile for tex editing, together with texlive
- I highly recommend Mendeley, one the best free reference managing software. It has online synchronization and allows you to access your database and PDF files through the webpage.
- For software development: Code::blocks or the complete Qt SDK (under free LGPL license)

Hi Marc and thanks for your contribution. I want to put two more references that you mentioned before:
- a program to extract data from a graph: http://www.frantz.fi/software/g3data.php
- physics engines: Open Dynamics Engine, you liked Bullet (modynamics uses bullet).
Cheers!

Ben, I found dead link on your updated version's link.

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