Concrete application of Jupyter and Jupyter extensions Jupyter

Concrete application of Jupyter and Jupyter extensions Jupyter lab, Jupyter. Hub, Binder. Hub Greg Versmee, MD, MS, MPH Open Access Week 2018

Topics covered • Write my first Jupyter Notebook • Install Jupyter on my local device • How to use Jupyter extensions: Jupyterlab, kernels, … • Share my work: install and use Jupyter on the cloud - Jupyter. Hub, Binder. Hub

bit. ly/jupyter-countway (deprecated after 10/23/2018)

My first Notebook

Install Jupyter Solution 1: Classic installation https: //jupyter. readthedocs. io/en/latest/install. html Solution 2: Containerized installation https: //github. com/jupyter/docker-stacks

Jupyter on Docker docker run -p 80: 8888 jupyter/minimal-notebook

Install Jupyter docker run -p 80: 8888 gversmee/jupyter 2 -full

Jupyter lab Jupyter. Lab provides a higher level of integration between notebooks, documents, and activities • Drag-and-drop to reorder notebook cells and copy them between notebooks • Run code blocks interactively from files (. py, . R, . md, etc. ) • Link a code console to a notebook kernel to explore code interactively • Edit popular file formats with live preview https: //blog. jupyter. org/jupyterlab-is-ready-for-users-5 a 6 f 039 b 8906

Jupyter lab

Jupyter + cloud computing Get the most of your Jupyter installation!

Install Jupyter https: //jupyterhub. hms. harvard. edu bit. ly/jupyter-countway (deprecated after 10/23/2018)

Jupyter. Hub, a multi-user Hub, spawns, manages, and proxies multiple instances of the single-user Jupyter notebook server. Jupyter. Hub can be used to serve notebooks to a class of students, a corporate data science group, or a scientific research group. https: //jupyterhub. readthedocs. io/en/stable/

Jupyter. Hub https: //zero-to-jupyterhub. readthedocs. io/en/stable/architecture. html

Binder. Hub • Creates custom computing environments from Git. Hub repositories • Binder. Hub serves the environment at a URL which users can access remotely • Can be used by many remote users, even without authentication • Public deployment available at https: //mybinder. org • Example: https: //github. com/gversmee/db. Ga. P 2 x https: //binderhub. readthedocs. io/en/latest/overview. html

Binder. Hub https: //binderhub. readthedocs. io/en/latest/overview. html

Questions? • How to request access to jupyterhub. hms. harvard. edu? - Send email to get whitelisted to: avillach_lab_developers@googlegroups. com • How to download files from your Jupyter environment created via docker? - Right click on the file to download it, or if necessary, use the docker cp command (https: //docs. docker. com/engine/reference/commandline/cp/) gregoire_versmee@hms. harvard. edu