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A Python package to simulate biochemical systems using the Constraint-Based Simulation Algorithm

Project description

Constraint-Based Simulation Algorithm (CBSA)

CBSA is a Python package for simulation of biochemical systems using the Constraint-Based Simulation Algorithm.

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Table of contents

Installation

CBSA can be installed on your computer using pip.

Just run the following command:

python3 -m pip install cbsa --user --upgrade

Usage

CBSA

Simple reaction example

Consider the following reaction system:

equation

Using the Constrain-Based Modeling, the Stoichiometric matrix becomes:

equation

A sample code to simulate this system is:

import cbsa
import matplotlib.pyplot as plt
import numpy as np

S = [[-1, 1, 0],
     [ 1,-1,-1],
     [ 0, 0, 1]]

init_mols = [50,0,0]
k = [0.5,0.1,0.8]
max_dt = 0.1
total_sim_time = 10

sim = cbsa.ReactionSystem(S)
sim.setup()
sim.set_x(init_mols)
sim.set_k(k)
sim.set_max_dt(max_dt)

sim.setup_simulation()
sim.compute_simulation(total_sim_time)
sim_data = np.array(sim.simulation_data)

plt.plot(sim_data[:,0],sim_data[:,1],label="A")
plt.plot(sim_data[:,0],sim_data[:,2],label="B")
plt.plot(sim_data[:,0],sim_data[:,3],label="C")
plt.legend()
plt.show()

example 1 image

License

CBSA is licensed under the MIT License. Please see the file LICENCE for more information.

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