Visualizing Dynamically Generated Protein Interactions

A Python library for visualizing dynamically generated protein interactions using 3D node-link layout.

DEMO Video

Installation

1. Clone the github repository

2. Requires anaconda and python=3.8

   conda create -n myenv python=3.8
   conda activate myenv
   

3. Install packages

   cd src/
   pip install -r requirements.txt
   

Note: You may need to install pygraphvis using conda forge: conda install --channel conda-forge pygraphviz (This may need a restart of your command prompt or terminal)

4. The data file in dot file format should be stored in

   ./src/visg/static/data/
   

5. Start server

   ./start-local.sh
   

6. Open browser (Google Chrome preferred)

   http://127.0.0.1:5001/index
   

Instructions to start the server

1. Change directory to ./src

   cd /path/to/project/src
   

2. Activate conda environment

   conda activate myenv
   

3. Start server

   ./start-local.sh
   

4. Open browser (Google Chrome preferred)

   http://127.0.0.1:5001/index
   

References

1. Libraries used: D3, Flask, 3d-force-graph