netplotlib

A package for visual analysis of biochemical reaction network models

Copyright 2018-2022 Kiri Choi

Introduction

Netplotlib is an extension to NetworkX and matplotlib for visual analysis of biochemical reaction network diagrams written in SBML or Antimony strings. Netplotlib supports visualization of quantities such as flux and species rate of change. Netplotlib provides functions to visualize an ensemble of biochemical reaction networks.

import netplotlib as npl

AntimonyStr = '''
$Xi -> S1; k0*Xi
S1 -> S2; k1*S1
S2 -> S3; k2*S2
S1 -> S3; k3*S1
S3 -> $Xo; k4*S3

Xi = 3; Xo = 2
k0 = 0.46; k1 = 0.73; k2 = 0.64;
k3 = 0.51; k4 = 0.22
'''
net = npl.Network(AntimonyStr)
net.draw()

Installation

To install, run the following command:

pip install netplotlib

Documentation

Documentation is available at https://netplotlib.readthedocs.io/en/latest

Examples