Python and Jupyter Notebook  
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This is a virtual workshop, you can participate by reading workshop materials, watching video presentations and carrying out exercises on an assigned BioHPC Cloud server (server assignments are listed here). If you need help, please sign up for our Office Hours. The server assigned to you for hands-on exercises will be available for a limited time, see server assignment page or bottom of this page for details. Please note, the server is assigned to you for hands-on exercises, NOT heavy computing, using the server for workshop unrelated computing is not allowed and will result in assignment termination.

This workshop does NOT teach you how to program in Python, but how to install and run Python software on a Linux computer. Running Python software used to be simple, and only years ago it would probably seem absurd that we offer a workshop teaching you how to do it. However, as the Python community growing bigger, Python ecosystem is getting a lot more complicated. The newly developed python scripts and packages are often very picky about the software environment in which they can run, for example, they would require specific versions of Python and libraries. One solution is to keep each Python software in its own isolated enviroment. The Introduction of Conda trys to address this problem, but also adds another layer of complexity into the system. In this workshop, we will go through the basics how Python manages its libraries, both the personal and shared python libraries. We will provide some practical tips of working with Python and Conda. We will also cover how to use Jupyter Notebook on the BioHPC system. Each workshop participant will be assigned a Linux computer to do exercises.

Lecture slides    Exercises(pdf version)   Exercises (html version)  Video recording

Workshop server assignment

Server assignment length 10 days  
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