Institute of Molecular Genetics

Oct 17 - 18, 2015

9:00 am - 5:00 pm

Instructors: Nasťa Zidkova, Filip Sedlák, Mira Hédl, Stefan Negru

Helpers: Petr Šimeček, Vašek Gergelits, Martin Jahn, Petr Švarný, Tomáš Laube, Charles Bajeux

General Information

This course will help you to use the computer more efficiently during your research. We'll show you how to automate repetitive procedures like manipulating files, computing statistics and creating charts from your data. This will help you make your analyses less error prone and reproducible.

If you're eager to learn but you don't see the use of such skills in your research, don't worry. The more you know, the more cases you'll see where you can apply your newly acquired skills.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Vídeňská 1083, Prague. Get directions with OpenStreetMap or Google Maps.

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

Price: This course is offered to you at courtesy of the instructors and helpers. Please smile at them. :-) There is no budget for food and beverages. If you'd like to return the favour, you're more than welcome to bring in any meal or snack.

Contact: Please mail for more information.

Registration: Registration is closed now :(


Don't take the schedule too seriously, it may change.

Day 1

09:00 Introductions
09:30 Introducing the Shell, Files and Directories
10:20 Coffee
10:40 Combining Shell Commands, Finding Things
12:00 Lunch break
13:00 Analyzing Patient Data in Python
14:30 Coffee
14:50 Making Choices, Combining Things, Understanding Errors
17:00 Wrap-up

Day 2

09:00 Defensive Programming, Debugging, Command-line programs
10:20 Coffee
10:40 Libraries in Python
12:00 Lunch break
13:00 Python project
16:00 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

Version Control with Git

  • Automated Version Control
  • Setting Up Git
  • Creating a Repository
  • Tracking Changes
  • Exploring History
  • Ignoring Things
  • Remotes in GitHub
  • Collaborating
  • Conflicts
  • Open Science
  • Licensing
  • Hosting
  • Reference...


To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Software Carpentry organization maintains a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option. This will provide you with both Git and Bash in the Git Bash program.

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.


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.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words.

The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows, Linux & Mac

We recommend you to install Atom or Sublime Text as your editor.


Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 2.x and not version 3.x (e.g., 2.7 is fine but not 3.4). Python 3 introduced changes that will break some of the code we teach during the workshop.

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).


  • Download and install Anaconda.
  • Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  • Download and install Anaconda.
  • Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation.


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 workshop.)

  1. Download the installer that matches your operating system and save it in your home folder. Download the default Python 2 installer (do not follow the link to version 3).
  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).

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.