ELIXIR Software Carpentry Workshop
Teaching basic lab skill for Research Computing
Du 28-03-2018 au 29-03-2018 à l'Institut Pasteur (Paris)
Date limite d'inscription: 24-03-2018




Allegra Via, TrC Elixir-Italy, IBPM-CNR

Kivan Polimis, Software Carpentry Instructor


Local organisers and Helpers

Victoria Dominguez Del Angel and Laurent Bouri, French Insitute of Bioinformatics UMS3601-CNRS, Campus Universitaire d'Orsay, France
Hervé Ménager, Pasteur Institute, Bioinformatics and Biostatistics Hub – C3BI, USR 3756 IP CNRS – Paris, France

Patricia Palagi (TrC Elixir-Switzerland, SIB)





Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. A maximum of 30 candidates will be selected based on their need for the course as emerging from the registration form. You don't need to have any previous knowledge of the tools that will be presented at the workshop, though we expect you are familiar with the most common Linux commands (e.g., ls, cd, mv, cp, rm, mkdir) and the main concepts/constructs used in programming (in any language) such as "variables", "functions", "loops" and "if conditions".

Fee: There is no course attendance fee. The participants will need to bear their travel, hotel (if any) . ELIXIR and IFB will cover coffee breaks and lunches costs. Registration is compulsory

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email victoria.dominguez[AT]france-bioinformatique.fr for more information.


Preliminary Program

Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
13:00 Lunch break
14:00 Version control with Git
14:30 Coffee
16:00 Wrap-up
17:30 END

Day 2

09:00 Building programs with Python
10:30 Coffee
13:00 Lunch break
14:00 Building programs with Python
14:30 Coffee
16:00 Wrap-up
17:30 END

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

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

Key Points

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



Video Tutorial

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". 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.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:
      setx HOME "%USERPROFILE%"
    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.



The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. 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.


Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.



Git should be installed on your computer as part of your Bash install (described above).



Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.



If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.


Key Points

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

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter 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).



Video Tutorial

  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.


Video Tutorial

  1. Open https://www.anaconda.com/download/#macos with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.


  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type

    >bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:

    >cd Downloads
    Then, try again.

  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. 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).
  6. Close the terminal window.


The registration is free of charge but compulsory

Fill up the following form if you wish to attend the event. Note that there is a limited amount of available slots. We will get back to you as soon as the selection process is over.

This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
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Solve this simple math problem and enter the result. E.g. for 1+3, enter 4.