International Symposium on Grids & Clouds (ISGC) 2018
in conjunction with
Frontiers in Computational Drug Discovery (FCDD)

16-23 March 2018, Academia Sinica, Taipei, Taiwan

EGI Jupyter Notebooks Tutorial: Interactive computing in the cloud

Date: Tuesday, 2 April 2019
Time: 11:15 – 17:30
Venue: Auditorium, 3F, Building for Humanities and Social Science, Academia Sinica


Gergely Sipos, Giuseppe La Rocca & Enol Fernandez, EGI Foundation


EGI Notebooks is a new service from the EGI e-infrastructure collaboration, providing a user-friendly and highly flexible Jupyter-based hosted environment for researchers to develop and share data analysis and visualisation ‘notebooks’. Notebooks can contain programming codes in various languages, HTML scripts, dynamic visualization and equations as well as images and explanatory text that provide guidance and context for the captured data analysis workflows. Through the notebooks users can easily share concepts, ideas and working applications, containing the full analytical methodology, connections to data sources, visualizations, and descriptive text to interpret those data. With the Binder ‘extension’ of Jupyter one can turn a Github repository with Jupyter notebooks into an executable environment, making code, visualisation and documentation immediately reproducible and reusable by anyone, anywhere. Jupyter and Binder are becoming pillars for Open Science.

This tutorial will introduce the open access EGI Notebooks service. The tutorial will go through the main features of the EGI Notebooks service and show how to use it with Binder for Open Science. Participants will experience the system through hands-on exercises written in Python based on real applications from the environmental sciences domain. The integrated use of Notebooks with EGI’s DataHub service will be also demonstrated. Communities or national e-infrastructures who would like to setup a similar service locally will be also informed about how to do this.

Outline of the tutorial:

Session 1

● Introduction to Jupyter and EGI Notebooks
● Login and hands-on exercises in Python

Session 2

● Introduction to Binder and GitHub
● Sharing and re-playing notebooks through GitHub - Hands-on

Session 3

● How to setup a local Notebook service? (talk)
● EGI Notebooks in the European Open Science Cloud context
● Advanced data management in Notebooks with EGI DataHub (talk + demo)

Target audience:

The tutorial is relevant for scientists, research IT support people, and system administrators who operate services for Open Science. The tutorial is introductory level, previous knowledge of EGI, Jupyter and GitHub is not required.