trellixvulnteam/neo4j-ipycytoscape_mlt7

Demo of Neo4j graph visualization with the ipycytoscape Jupyter Lab extension

neo4j-ipycytoscape

This repo demonstrates how to use the ipycytoscape widget to visualize a Neo4j subgraph with cytoscape.js in JupyterLab and the Jupyter notebook.

Notebook	Description
Neo4j_Example1	Creates a small Neo4j graph locally and demonstrates how to display a Neo4j subgraph
Neo4j_Example2	Accesses the COVID-19-Net Knowledge Graph server and demonstrates how to display a Neo4j subgraph

Run Jupyter Lab locally

Follow the steps below to setup and run the example notebooks on Mac, Linux, or Windows.

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Prerequisites: Miniconda3 (light-weight, preferred) or Anaconda3 and Mamba

• Install Miniconda3
• Update an existing miniconda3 installation: conda update conda
• Install Mamba: conda install mamba -n base -c conda-forge
• Install Git (if not installed): conda install git -n base -c anaconda

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1. Clone this Git repository

git clone https://github.com/sbl-sdsc/neo4j-ipycytoscape.git
cd neo4j-ipycytoscape

2. Create a Conda environment

The file environment.yml specifies the Python version and all packages required by the tutorial.

mamba env create -f environment.yml

Activate the conda environment

conda activate neo4j-ipycytoscape

3. Launch Jupyter Lab

jupyter lab

Navigate to the notebooks directory to run the example Jupyter Notebooks.

4. Deactivate the Conda environment

When you are finished, deactivate the conda environment or close the terminal window.

conda deactivate

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To remove the Conda environment, run conda env remove -n neo4j-ipycytoscape

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Run Jupyter Lab in your web browser using Pangeo Binder

NOTE: Authentication is required to launch binder! Sign into GitHub from your browser, then click on the launch binder badge below to launch Jupyter Lab.

Pangeo Binder is unsupported and may not always be available or slow. Launching Jupyter Lab may take a few minutes.

Run Jupyter Lab on SDSC Expanse

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Prerequisites:

• XSEDE account
• Expanse allocation
• Append export PATH="/cm/shared/apps/sdsc/galyleo:${PATH}" to your .bashrc on Expanse and run source ./.bashrc

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1. Log into the Expanse Portal with your XSEDE credentials.

2. Open a Terminal Window ("Shell Access") through the Expanse Portal

3. Clone the Git repository neo4j-ipycytoscape

git clone https://github.com/sbl-sdsc/neo4j-ipycytoscape.git

4. Launch Jupyter Lab using the Galyleo

   Fill in the your project account number in the command below.

   This script will generate a URL for your Jupyter Lab session.

galyleo launch --account <account_number> --partition shared --cpus 4 --memory 8 --time-limit 00:30:00 --conda-env neo4j-ipycytoscape --conda-yml "${HOME}/neo4j-ipycytoscape/environment.yml" --mamba

5. Open a new tab in your web browser and paste the Jupyter Lab URL.

You should see the Satellite Reserver Proxy Servive page launch in your browser.

Wait until Jupyter Lab launches. This may take several minutes.

6. Run the example notebooks

   Navigate to the notebooks directory to run the example Jupyter Notebooks.

7. Shutdown Jupyter Lab

   From the file menu select Shutdown to terminate the process.

If you do not shutdown Jupyter Lab, the process will continue running and use up allocated resources.

Citation

Peter W. Rose, David Valentine, Ilya Zaslavsky, COVID-19-Net: Integrating Health, Pathogen and Environmental Data into a Knowledge Graph for Case Tracking, Analysis, and Forecasting. Available online: https://github.com/covid-19-net/covid-19-community (2020).

Funding

The Neo4j graph visualization for ipycytoscape is in part supported by the National Science Foundation under Award Numbers:

NSF Convergence Accelerator Phase I (RAISE): Knowledge Open Network Queries for Research (KONQUER) (1937136)

NSF RAPID: COVID-19-Net: Integrating Health, Pathogen and Environmental Data into a Knowledge Graph for Case Tracking, Analysis, and Forecasting (2028411)