This page is dedicated to the software I use and has an install script at the bottom for getting it installed on a fresh machine. I plan to keep this page updated, but for the software that is downloaded via wget you should check yourself whether I’m referring to the latest version. Here’s a brief description of my favourites (alphabetical order).

    • Bitbucket/GitHub: Version control hosting for Git and Mercurial (not really software!)
    • Feedly: Collect your news via RSS
    • Geany: Text editor
    • Git: Version control software
    • GRASS: Geographic information system (GIS)
    • JabRef: Reference database
    • QGIS: Geographic information system (GIS)
    • Nextcloud: cloud storage for Linux, Windows, Android, etc.
    • R: Statistical and programming software
    • RStudio: Development environment for R
    • Scribus: Desktop publishing
    • SQLite: Easy, lightweight database
    • Texmaker: LaTeX document writer

My operating system of choice is Ubuntu, which is built on Linux (like Android is). I also use a lightweight Ubuntu derivative, Lubuntu, on my laptop as it is much less resource heavy. Being an Ubuntu derivative means I can install all the same software as my desktops, and only need a mildly modified version of the below script for installing software. A lot of the software on this page is available for Windows and Macs, but it is all available for Debian like Linux systems like Ubuntu. I switched from using Windows to Ubuntu in early 2011 and have not regretted the decision. I have it installed on my home and work desktops and also my laptop, it’s great having all machines running the same operating system with the same software installed and access to the same files and folders (the latter via Nextcloud and rsync). You can read more about using Ubuntu and some of the above software for science on John Stevenson’s blog.

Some of the software I use falls under the umbrella of OSGeo, which is an organisation that looks after spatial software like GRASS and QGIS. They maintain an image operating system containing all their spatial projects. If you want to try some out, this is an excellent place to start. OSGeo also has country specific chapters; as most of my blog readers are from the UK here is the UK OSGeo chapter. The local chapters are great for putting you in touch with other users and as a place to ask advice and find assistance.

To install the above (and other useful things) on a Debian (Ubuntu) like system, paste the following commands into a terminal. The script is tailored for the latest Long Term Support (LTS) version of Ubuntu (16.04, Xenial Xerus) in 64bit, so will likely need adapting for other versions. The copy and paste is probably best done in chunks split by the comments (#), which also divide it into different software types. The script below requires web access to download software, and you will also be prompted for your password to install new software.

# Cloud
sudo apt-key add - < Release.key
rm Release.key
sudo sh -c "echo 'deb /' >> /etc/apt/sources.list.d/owncloud-client.list"
sudo apt-get update
sudo apt-get install owncloud-client

# General
sudo add-apt-repository 'deb xenial partner'
sudo apt-get install geany byobu p7zip-full gimp pdfshuffler scribus \
filezilla lftp ubuntu-restricted-extras vlc pyrenamer imagemagick hugin \
darktable skype handbrake libdvd-pkg avidemux

# Remove things I don't want
sudo apt-get remove aisleriot gnome-mahjongg gnome-sudoku gedit

# Data processing
sudo apt-key adv --keyserver --recv-keys E084DAB9
sudo add-apt-repository 'deb xenial/'
sudo apt-get update
sudo apt-get install spyder python-numpy python-numpy-doc sqlite3 \
python-scipy python-matplotlib python-matplotlib-doc r-base git-core meld
# Add your own name and email
git config --global "Your Name" && git config --global ""

# Maps and GIS software
sudo apt-get install python-software-properties
sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install grass grass-doc grass-dev qgis python-qgis libgdal1-dev \
libproj-dev gpsbabel

# Referencing manager and ibus to make Texmaker (LaTeX) work
sudo apt-get install jabref qt5-default texlive texlive-latex-extra \
texlive-humanities texlive-fonts-extra latex-beamer texlive-xetex

# Package download and install (Texmaker and RStudio)
sudo dpkg -i *.deb
sudo apt-get -f install
sudo dpkg -i *.deb
rm *.deb



  1. Two questions:
    * I’m curious what your primary “scientific” use of Scribus is. I just made a poster in latex/beamer, and I’d say that’s the most complex “page layout” I do. I’m guessing your use of scribus is complementary to latex, just not sure what for?
    * Any thoughts on Spider Oak versus Dropbox versus Copy? I’ve had a free dropbox account for ages, but I probably won’t upgrade with them. I’m just starting to learn spideroak, and thinking about buying into it as a long-term solution — great documentation and a rich feature-set, including auto-versioned backup and restore. Am I correct to view Copy as a somewhat less expensive dropbox clone/alternative with a killer small business plan?

    1. Thanks for reading.

      There are many ways to approach the same task. Currently I prefer scribus for layout work, although I have colleagues who use LaTeX for everything!

      I moved to copy recently, as Ubuntu one cloud storage is/was being retired. Reason I chose it was the large free storage and good Linux integration. So far I’ve been very pleased with it. I handle my backups semi manually using rsync, no matter how good the cloud service I wouldn’t want to trust it completely. I once had a problem with computer clocks being out which led to a lot of files automatically being deleted from my cloud store.

      I should also say that copy seems to work well holding git repos, which is useful as I work across three different machines. I let copy handle syncing the files and then push them out as I progress.

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