SimBio: Simulation of Biological Systems

simbio is a Python-based library of biological systems simulation. It allows to define, inspect, compile and simulate models.

Installation

Using pip, it can be installed directly from PyPI:

pip install simbio

or install the latest development version from GitHub:

pip install git+https://github.com/hgrecco/simbio

Table of contents

Definition

• Model creation
• Static or class-based
• Dynamic or programmatic
• Defining new reactions

Compilation

• Compilers

Examples

• Basic
• Enzymatic
• Multiple compartments
• Chained reactions