e-learning
Use Jupyter notebooks in Galaxy
Abstract
In this tutorial, we are going to explore the basics of using JupyterLab in Galaxy. We will use the Gapminder data as a test set to get the hang of Jupyter notebooks. The python-novice-gapminder-data.zip file is publicly available. This tutorial can also be used as an initial setup for the Software Carpentries training Plotting and Programming in Python.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How to open a Jupyter Notebook in Galaxy?
- How to update dependencies in a Jupyter Interactive Environment?
- How to save and share results in the Galaxy History?
Learning Objectives
- Learn about the Jupyter Interactive Environment
- Load data into a Jupyter Interactive Environment
- Install library dependencies
- Save a notebook to the Galaxy history
Licence: Creative Commons Attribution 4.0 International
Keywords: Using Galaxy and Managing your Data
Target audience: Students
Resource type: e-learning
Version: 10
Status: Active
Prerequisites:
- Galaxy Basics for genomics
- Understanding Galaxy history system
Learning objectives:
- Learn about the Jupyter Interactive Environment
- Load data into a Jupyter Interactive Environment
- Install library dependencies
- Save a notebook to the Galaxy history
Date modified: 2025-05-11
Date published: 2018-07-02
Contributors: Björn Grüning, Bérénice Batut, Delphine Lariviere, Helena Rasche, Lisanna Paladin, Niall Beard, Nicola Soranzo, Saskia Hiltemann, Teresa Müller
Activity log
