University of Southern Denmark

Room U24 on day 1, room U30A on day 2
Apr 3-4, 2014
9:00 am - 5:00 pm

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Instructors: Luis Pedro Coelho, Steven Koenig

Who: The course is aimed at graduate students and other researchers.

Signup link:

Where: Room U24 on day 1, room U30A on day 2. To travel from the station to the University of Southern Denmark (SDU) main campus, take bus 41 or 42 from the Odense train station terminal. The buses run Mondays to Fridays from 7:30 to 19:30 about every 10 minutes. The transit time is around 22 minutes. Outside these times they run less frequently. You can get off at the first stop at the university and use the main entrance. To view a map of the area you can use OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail for more information.


The workshop materials are now available online. Also, we would like to draw your attention to further lessons online:

Day 1 (Apr 3) 09:00-10:30 Introduction to task automation with a Unix shell
11:00-12:30 Introduction to regular expressions
12:30-13:30 Lunch break
13:30-15:00 Building programs with Python (I)
15:30-17:00 Building programs with Python (II)
Day 2 (Apr 4) 09:00-10:30 Automated testing of Python Programs
11:00-12:30 Version control with Git
12:30-13:30 Lunch break
13:30-15:00 Version control with Git
15:30-16:15 SQL
16:15-17:00 Open Q&A, Wrap-up


To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.


The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.


Git is a state-of-the-art version control system. It lets you track who made changes to what when and has options for easily updating a shared or public version of your code on


Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.


SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.


Software Carpentry Installer

For an all-in-one installer:

  • Download the installer.
  • If the file opens directly in the browser select File→Save Page As to download it to your computer.
  • Before you can double click on the file to run it, you will need to set up two things on your own.
    1. Install Python. See the instructions for installing Python on this page on how to do this.
    2. Install Git for Windows. Install the version linked to on this page (1.8.4).

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.


Download the GnuWin32 binary package for make and save it on your Desktop.

If you are not sure how to do the next steps, do not continue, we will help you install it at the workshop.

  1. Make sure that you have Git Bash installed (see above).
  2. Open the ZIP file of the GnuWin32 binary package for make. You should see the folders bin, contrib, man, manifest and share. If not, do not continue.
  3. Copy all those folders.
  4. Git Bash should have been installed into C:\Programs\Git or C:\Program Files\Git. Open up that folder in an Explorer window.
  5. You should see folders like bin, cmd, doc, etc, lib, man. If not, do not continue.
  6. Paste here, Windows will ask you if you really want to paste folders with the name, which you want.


  • Download and install Anaconda CE.
  • Use all of the defaults for installation except make sure to check Make Anaconda the default Python.


Download the sqlite3 program and put it in the directory where you are running examples. Alternatively, you may install the Firefox SQLite browser plugin described below.

Mac OS X


The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.


Install Git for Mac by downloading and running the installer.


make is included in Apple's Development Resources. See the link on the right side saying 'Command Line Tools'. You will need to sign up there. Follow the instructions to install the Command Line Tools.


  • Download and install Anaconda CE.
  • Use all of the defaults for installation except make sure to check Make Anaconda the default Python.


sqlite3 comes pre-installed on Mac OS X. Alternatively, you may install the Firefox SQLite browser plugin described below.



The default shell is usually bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.


If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).


sqlite3 comes pre-installed on Linux. Alternatively, you may install the Firefox SQLite browser plugin described below.


We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window.
  3. Type
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).


Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you may use this plugin for Firefox instead. To install it:

  • Start Firefox.
  • Go to the plugin homepage.
  • Click the "Add Now" button.
  • Click "Install Now" on the dialog that appears after the download completes.
  • Restart Firefox when prompted.
  • Select "SQLite Manager" from the "Tools" menu.