SimBio 0.2.0

Simulation of Biological Systems

SimBio

simbio is a Python-based library of biological systems simulation. As a comparison with other libraries we can enumerate:

• Models are composables, so you can create bigger models using smaller ones
• Models are python classes, so it is easier to understand the inners and easy to compose into bigger models
• Posibility to do numba JIT compilation
• Small footprint library, can be imported on a bigger application without fuzz

Installation

If you are using pip, it can be installed directly from PyPI:

pip install simbio

or the latest version from GitHub:

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

Examples

On the folder src/simbio/tests/examples, we included some examples for the library usage.

Development

We are using pytest for testing, and pre-commit hooks to format and lint the codebase.

To easily set-up a development environment, run the following commands:

git clone https://github.com/hgrecco/simbio
cd simbio
conda env create --file environment-dev.yml
pre-commit install

which assume you have git and conda preinstalled.