Creates reaction graph for NeuroRD tool: https://github.com/neurord/stochdiff

Features

Creating reaction graph in the web browser.

• square - represents molecule
• diamond - represents reaction
• arrow direction - represents the forward direction
• arrow thickness - represents value of the reaction that represents its color

Edge colors:

• green - represents domination of the forward rate
• red - represents domination of the reverse rate

Square colors:

• blue - regular particle
• yellow - (if selected) key particles from reactants

Prerequisites

pip install -r requiremets.txt

Run

python create_reaction_graph.py --reaction_file [FILE] 

• reaction_file - is the XML reaction file created for NeuroRD tool
• By default all results are created inside reaction_visualizations/ volder

Example graph

This is the example graph of all reactions of CaMKII kinase from the dendritic spine in the CA1 hippocampal cell

In the examples folder/ :

• graph.html - interactive graph to play, shows all reactions of CaMKII (denoted as CK)
• graph.gif - gif shows the same graph