Metadata-Version: 2.1
Name: cbsa
Version: 0.0.4
Summary: A Python package to simulate biochemical systems using the Constraint-Based Simulation Algorithm
Home-page: https://github.com/pauloburke/CBSA
Author: Paulo Burke
Author-email: pauloepburke@gmail.com
License: UNKNOWN
Description: # Constraint-Based Simulation Algorithm (CBSA)
        
        CBSA is a Python package for simulation of biochemical systems using the Constraint-Based Simulation Algorithm.
        
        
        [![PyPI](https://img.shields.io/pypi/v/cbsa.svg?color=b44e48)](https://pypi.org/project/cbsa)
        ![PyPI - License](https://img.shields.io/pypi/l/cbsa.svg?color=lightgray)
        ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/cbsa.svg?color=lightgreen)
        
        Table of contents
        -----------------
        
        * [Installation](#installation)
        * [Usage](#usage)
        * [License](#license)
        
        
        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](https://latex.codecogs.com/gif.latex?A%20%5Cleftrightarrow%20B%20%5Crightarrow%20C)
        
        Using the Constrain-Based Modeling, the Stoichiometric matrix becomes:
        
        ![equation](https://latex.codecogs.com/gif.latex?S%20%3D%20%5Cbegin%7Bbmatrix%7D%20-1%20%26%201%20%26%200%20%5C%5C%201%20%26%20-1%20%26%20-1%20%5C%5C%200%20%26%200%20%26%201%20%5Cend%7Bbmatrix%7D)
        
        A sample code to simulate this system is:
        
        
        ```python
        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](docs/images/example_1.png)
        
        
        License
        -------
        
        CBSA is licensed under the MIT License.  Please see the file [LICENCE](LICENSE) for more information.
        
        
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
