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https://github.com/sbl-sdsc/neo4j-ipycytoscape
Demo of Neo4j graph visualization with the ipycytoscape Jupyter Lab extension
https://github.com/sbl-sdsc/neo4j-ipycytoscape
cytoscape graph-visualization ipycytoscape knowledge-graph neo4j property-graph
Last synced: about 1 month ago
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Demo of Neo4j graph visualization with the ipycytoscape Jupyter Lab extension
- Host: GitHub
- URL: https://github.com/sbl-sdsc/neo4j-ipycytoscape
- Owner: sbl-sdsc
- License: bsd-3-clause
- Created: 2020-04-20T00:24:12.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-09-29T23:18:00.000Z (over 1 year ago)
- Last Synced: 2023-09-30T12:09:09.324Z (over 1 year ago)
- Topics: cytoscape, graph-visualization, ipycytoscape, knowledge-graph, neo4j, property-graph
- Language: Jupyter Notebook
- Homepage:
- Size: 136 KB
- Stars: 3
- Watchers: 2
- Forks: 5
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# neo4j-ipycytoscape
This repo demonstrates how to use the [ipycytoscape widget](https://github.com/QuantStack/ipycytoscape) to visualize a Neo4j subgraph with cytoscape.js in Jupyter Lab. It also demonstrates how to setup a local instance of the Neo4j graph database and launch Neo4j Browser from a Notebook.
Example subgraph rendered in Jupyter Notebook.
Colors and styles of nodes and relationships can be changed. By clicking on a node, a tooltip with the node properties is displayed. The layout can also be manually changed by dragging nodes to new positions.
|Notebook|Description|
|:-------|:----------|
|[Neo4j_Example1](notebooks/Neo4j_Example1.ipynb)| Creates a small Neo4j graph locally and demonstrates how to display a Neo4j subgraph|
|[Neo4j_Example2](notebooks/Neo4j_Example2.ipynb)| Accesses the [COVID-19-Net Knowledge Graph](https://github.com/covid-19-net/covid-19-community) 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.
------
Prerequisites: Miniconda3 (light-weight, preferred) or Anaconda3 and Mamba (faster than Conda)
* Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html)
* 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```
------
**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`](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
```
------
> To remove the Conda environment, run ```conda env remove -n neo4j-ipycytoscape```
------
## Run Jupyter Lab on SDSC Expanse
[Expanse](https://www.sdsc.edu/support/user_guides/expanse.html) is an National Science Foundation (NSF)-funded supercomputer at the [San Diego Supercomputer Center](https://www.sdsc.edu/) at UC San Diego. Free allocations are available for academic researchers. A trial allocation can be obtained by contacting [email protected] or a full allocation by applying through the [ACCESS progam](https://allocations.access-ci.org/prepare-requests-overview).
1. Log into the [Expanse Portal](https://portal.expanse.sdsc.edu/) with your ACCESS credentials.
2. Open a Terminal Window ("Shell Access") through the [Expanse Portal](https://portal.expanse.sdsc.edu/).
3. Clone the Git repository neo4j-ipycytoscape
```
git clone https://github.com/sbl-sdsc/neo4j-ipycytoscape.git
```
4. Change into the neo4j-ipycytoscape directory
```
cd neo4j-ipycytoscape
```
5. Launch Jupyter Lab using the Galyleo
Fill in the your project account number in the command below. Galyleo will generate a URL for your Jupyter Lab session and create a Conda environment specified by the environment.yml file.
```
galyleo launch --account --partition shared --cpus 1 --memory 8 --time-limit 00:30:00 --conda-env neo4j-ipycytoscape --conda-yml environment.yml --mamba
```
> Note, before you use Galyleo the first time, append ```export PATH="/cm/shared/apps/sdsc/galyleo:${PATH}"``` to the ```.bashrc``` file in your home directory then and run ```source ./.bashrc```.
6. Open a new tab in your web browser and paste the Jupyter Lab URL.
Wait until Jupyter Lab launches. This may take several minutes.
> You should see the Satellite Reserver Proxy Servive page launch in your browser.
8. Run the example notebooks
Navigate to the [`notebooks`](notebooks) directory to run the example Jupyter Notebooks.
9. 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 was 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](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1937136))
**NSF RAPID:** COVID-19-Net: Integrating Health, Pathogen and Environmental Data into a Knowledge Graph for Case Tracking, Analysis, and Forecasting ([2028411](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2028411))