Tutorial on Reproducible Research for the SyncFree Project


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After my tutoriel at Compas, Marc Shapiro kindly invited me to give another tutorial to the PhD students of the SyncFree Europen project. There were about 8-9 people, mainly 1st or 2nd year PhD students and Annette Middelkoop-Bieniusa, the project coordinator.

The purpose of this tutorial was:

  1. To give an overview of current trends in reproducible research,
  2. To demonstrate that R/knitr or R/org-mode are perfectly usable for doing reproducible analysis and that there is no more excuse for not doing it… ;)
  3. To show how to use emacs/org-mode for keeping a laboratory notebook.

To make sure everyone would have a working environment, I decided to learn to use Kameleon to set up well set up Virtual Machines. There are two alternatives:


If you're running linux, you probably want to use this VM (debian_test.qcow2), which can be run as follows:

      sudo qemu-system-x86_64 -m 2048 --enable-kvm debian_test.qcow2

If you're running Mac OS X, you can choose the easy was (i.e. use the VirtualBox image) or the hard one (use the QEMU image). Joseph Emeras told me it was possible to get qemu 2.0.0 by installing brew (http://brew.sh/) and then brew install qemu.

If you're running on Mac OS X, you probably want to use this VM (debian_test.vdi). You may want to select the mac keyboard layout once logged in. Also make sure you give enough RAM (e.g., 2GB) to the VM if you want to be able to work with it and possibly make a large data analysis. Here are roughly what the steps are for running it:
  • Run VirtualBox
  • Click the "New" button
  • Enter the name "PUF/JLPC VM";
  • Select "Linux" with the OS Type dropdown and "Debian (64 bit)" with the Version drowdown
  • Select "Next"
  • On the "Memory" panel, increase to at least 2GB and select "Next"
  • On the Virtual Hard Disk panel select "Existing" and then select the file with the small icon
  • Select the "debian_test.vdi" file that you just downloaded
  • Click "Open", "Create" and you're all set
  • Run the VM by double-clicking on it

These VM are recent debian images with

This VM stuff was partly successful and here are a few issues to fix:

Here are the slides I used. Everything went smooth except the video projector died after one hour. When we finally went to another room, there was some power surge when I plugged my AC adapter (hopefully, my laptop was intact) and the projector was not working either… :( Bad luck. Demoing rstudio and emacs without projectors was quite painful and I did lost some people here…

A few things to improve for the next time: