Generate CellML from BG-RDF models

Warning

These tools are actively being developed and nothing should be considered stable until version 1.0 has been released.

Installation

As a package

uv add https://github.com/CellDL/BG-Tools/releases/download/v0.9.2/bg2cellml-0.9.2-py3-none-any.whl

Development

$ git clone https://github.com/CellDL/BG-Tools
$ cd BG-Tools
$ git submodule update --init --recursive
$ uv sync --all-groups

Usage

See cli/bgtool/__main__.py for details.

Example models:

• An RC electrical circuit
• A simple biochemical reaction
• All examples

Examples in a Jupyter notebook:

1. Clone the repository and its sub-modules as above.
2. Install with uv sync --group notebook
3. Start JupyterLab with uv run jupyter lab
4. Open ./notebooks/bg2cellml.ipynb in Jupyter.