Case Notebook

An environment for authoring and playing simulated clinical cases.

Directory Map

• basics - Contains examples of basic technologies used in the project. Each technology is addressed by a directory. This direct has only learning purposes, i.e., it does not contain any code of the system.

• binder - Binder environment setup, as you can launch Jupyter under Binder to test some aspects of this project. In the previous version, the authoring environment was implemented under Jupyter; in the current version, the Jupyter is used to run examples in the [basics] directory.

• data - Data sources that support the development and execution of clinical cases. Examples: ontologies (e.g., MeSH); Zombie Health support data.

• notebook - Main directory, it contains the code of the whole notebook (client and server). This directory is detailed at: Notebook README.

• player-interface - Design essays of the player interface.

Getting Started

Option 1: Access an instance running at our cloud

The link below starts the authoring environment running in our cloud

• http://cloud.lis.ic.unicamp.br/case-notebook/v1/web/author/author.html

Option 2: Run a local instance as a Docker container

Make sure you have Docker and docker-compose installed, then start the container directly:

sudo docker run -it -p 80:80 -p 8888:8888 datasci4health/case-notebook 

Or via docker-compose:

sudo docker-compose --url https://github.com/datasci4health/case-notebook/blob/master/docker-compose.yml up

After starting the container, got to http://localhost/author/author.html to see the authoring environment.

Option 3: Running Jupyter Locally

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Instructions to install Jupyter and Case Notebook in your machine:

Linux Installation

PIP3 installation

sudo apt-get update
sudo apt-get install python3-pip

Jupyter installation

pip3 install jupyter

Jupyter will be probably installed in the following directory;

~/.local/

Download the Git project in the suggested directory

~/git/case-notebook/

Libraries installation

SPARQLWrapper

pip3 install SPARQLWrapper

Widgets

pip3 install ipywidgets
sudo ~/.local/bin/jupyter nbextension enable --py widgetsnbextension

Kernel Gateway (for Python REST services)

pip3 install jupyter_kernel_gateway

Case-Notebook extension installation

cp -r ~/git/case-notebook/nbextensions/notebook/case-notebook ~/.local/share/jupyter/nbextensions
sudo ~/.local/bin/jupyter nbextension install ~/.local/share/jupyter/nbextensions/case-notebook/
sudo ~/.local/bin/jupyter nbextension enable case-notebook/main

Starting Jupyter

~/.local/bin/jupyter notebook

Windows Installation

Python and PIP3 instalation

Install latest version of Python 3. It comes with PIP3. For python 3.7, it will be probably be installed in the following directory:

C:\Program Files\Python37

Jupyter installation

Considering that Python is in your PATH (and consequently PIP3), open a terminal as admnistrator and type:

pip3 install jupyter

Download the Git project in the suggested directory

/Users/<User>/git/case-notebook

Libraries installation

Considering that Python is in your PATH (and consequently Jupyter), type the following commands to install the libraries:

SPARQLWrapper

pip3 install SPARQLWrapper

Widgets

pip3 install ipywidgets
sudo ~/.local/bin/jupyter nbextension enable --py widgetsnbextension

Kernel Gateway (for Python REST services)

pip3 install jupyter_kernel_gateway

Case-Notebook extension installation

xcopy C:\Users\<User>\git\case-notebook\notebook\nbextensions\* "C:\Program Files\Python37\share\jupyter\nbextensions" /s
jupyter nbextension install "C:\Program Files\Python37\share\jupyter\nbextensions\case-notebook"
jupyter nbextension enable "C:\Program Files\Python37\share\jupyter\nbextensions\case-notebook\main"

Starting Jupyter

jupyter notebook