Welcome to PyEnzyme’s documentation!#

PyEnzyme is the interface to the data model EnzymeML and offers a convenient way to document and model research data. Lightweight syntax for rapid development of data management solution in enzymology and biocatalysis.

Get started with PyEnzyme by running the following command

# Using PyPI
python -m pip install pyenzyme

Or build by source

git clone https://github.com/EnzymeML/PyEnzyme.git
cd PyEnzyme
python3 setup.py install

Package Options#

PyEnzyme comes with many flavors, choose whether you want only the base installation, the modeling package or all of it using the following options.

# COPASI - modeling
python -m pip install "pyenzyme[copasi]"

# PySCeS - modeling
python -m pip install "pyenzyme[pysces]"

# Modeling package
python -m pip install "pyenzyme[modeling]"

python -m pip install "pyenzyme[rest]"

# Dataverse
python -m pip install "pyenzyme[dataverse]"

# Complete
python -m pip install "pyenzyme[all]"


If you want to deploy PyEnzyme as a server and use our REST-API to access PyEnzyme from any HTTP-capable programming language, use our official docker image or simply copy and past the following.

docker pull enzymeml/pyenzyme:latest
docker run -p 8000:8000 enzymeml/pyenzyme:latest

See the API documentation for details on our endpoints. You can also use our self-hosted PyEnzyme instance if you have no server space - Use https://enzymeml.sloppy.zone as base URL to the endpoints.

Table of contents#

Indices and tables#