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PyEnzyme
v1.1.5 Build Badge Documentation Status

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.

🧬 Features

  • Reproducible documentation of enzymatic and biocatalytic experiments.
  • Import from and export to the SBML-based markup language EnzymeML and more.
  • Perform database-specific validation prior to database upload.
  • Model your data using a Thin Layer to popular modeling platforms.
  • Visualize experimental results for inspection and publication.

⚡️ Quick start

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]"

# REST API
python -m pip install "pyenzyme[rest]"

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

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

⚙️ Example code

This example will demonstrate how to create a simple EnzymeML document using PyEnzyme and how to use initializers from official databases Chebi and UniProt to gather metadata. For more examples, please visit our documentation (Work in progress)

# To be added for V2

(Code should run as it is)

📖 Documentation and more examples

Explore all the features of PyEnzyme in our documentation and take part in Discussions and/or Issues.

⚠️ License

PyEnzyme is free and open-source software licensed under the BSD 2-Clause License.

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🧬 - Data management and modeling framework based on EnzymeML.

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