18/06/2017 - 20/06/2017

Humboldt University, Berlin
Berlin, Germany

Software Carpentry

Code: 2017-SWC-Berlin
Price: free
Location: Humboldt University, Berlin
Available seats: 40


Please visit the course homepage for more information and registration


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.

 The two-day programme will cover Bash and shell scripting, version control with git and GitHub, and an introduction to programming with Python.

Topics covered include:

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…

Learning goals:
This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible.

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. 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.