Jupyter Notebooks and Associated Public Content 2019

Launch the Notebooks Interactively. Click here =>

Binder is a service that turns a Git repo into a collection of interactive notebooks.
You'll enjoy the experience of Jupyter Dashboard and notebooks in the cloud.

Local users on JupyterHub - download notebooks using Jupyter Terminal

• Sign in at https://jupyter.cscscience.ca with Science Network user/password
• Click the '+' in the upper left, scroll down to Other
• Open a Terminal and enter the below command to download and make available the notebooks:
  wget --content-disposition "https://github.com/TheZetner/jupyter-examples-2019/archive/v0.2.zip" -O jupyter.zip; unzip jupyter.zip; while read p; do pip install --user $p; done < jupyter-examples-2019-0.2/requirements.txt
• Sometimes jupyter hub can have issues like File load errors (it's not a core resource and has no designated IT staff) but the easiest way to fix those is to open up a jupyter terminal as above and kill your user's processes on jupyter then refresh the page and follow the prompts: killall -u YOURSCIENCEUSERNAME

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Run the notebooks on Microsoft Azure

Azure is a similar service as Binder allowing the user to run jupyter notebooks with a limited number of kernels.

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See the Gists

• Gists are single files, parts of files, and full applications to easily share with other people.
• Directories can't be shared
• Gists can be public or private
• Gists are editable in place
• Gists are repositories that can be forked and cloned
• More about Gists

Example Jupyter Notebook with R:

Repository

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Leave Feedback and View the Slides

Slides are available after the workshop as thanks for filling out the feedback form!

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Other Resources

Please don't read these while I present. I'll definitely know </3.

Reproducibility

• Nature article on reproducibility
• More recent Nature article on Jupyter as a data science tool
• Reproducible Research

Markdown

• Markdown Cheatsheet
• Markdown, the Jupyter guide

Data Science

• The unreasonable effectiveness of public work - David Robinson
• I don’t like notebooks - Joel Grus
• Eliademy: Open Research Software and Open Source
• DOI Numbers and Citable Code with Github
• Open source licenses

Jupyter Links

• Online resources to run jupyter
• Jupyter Project home
• 10 Rules for working in jupyter notebooks
• Combining interactivity and reproducibility: Can Jupyter Notebooks Serve Two Masters? Amanda Birmingham
• Jupyter project and notebook organization

Jupyter Sources

• https://www.dataquest.io/blog/jupyter-notebook-tutorial/
• https://www.slideshare.net/lynnlangit/jupyter-notebooks-by-bioinformatics-examples
• https://reproducible-science-curriculum.github.io/publication-RR-Jupyter/
• https://github.com/jupyter-guide/ten-rules-jupyter
• https://github.com/jupyter-guide/jupyter-guide

Jupyter Lab

• Jupyter’s Next-Generation Notebook Interface: LINK
• JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data.
• JupyterLab is flexible: configure and arrange the user interface to support a wide range of workflows in data science, scientific computing, and machine learning.
• JupyterLab is extensible and modular: write plugins that add new components and integrate with existing ones.
• Activate in binder file explorer by changing end of url from /tree to /lab

Notebook Extensions

• Notebook Extensions

• Enable nbextensions
  conda install -c conda-forge jupyter_nbextensions_configurator

• Enable nbextensions
  jupyter nbextensions_configurator enable --user

• Make Repo for notebooks, get personal access token from github

• Go to Nbextensions tab on dashboard

• Activate GIST-IT, add your access token

• Click gistit button on notebook

• An interesting looking extension to track exploration history: https://github.com/mkery/Verdant