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]"

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

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

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

REST-API

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

First Steps

• Setting up an EnzymeML document
  • Documentation of a simple single substrate reaction
  • Building the reaction network
    • Creating reactions from equations
    • Adding the reaction to the document
  • Documenting measurement setups
  • Adding experimental raw data
  • Saving and distributing an EnzymeML document
• Loading and editing
• Validation of EnzymeML documents
  • Generation and conversion of a validation spreadsheet
  • Using an example spreadsheet
  • Performing validation
• Visualisation of an EnzymeML document
  • Visualising all measurements
    • Static
    • Interactive
    • One last thing
• Upload to Dataverse

Examples

• Modeling a reaction by mass action cascades using PySCeS

API Reference

• Core layer
  • EnzymeMLDocument
  • Creator
  • Vessel
  • Reactant
  • Protein
  • EnzymeReaction
  • Measurement
  • MeasurementData
  • Replicate
  • Unit Definition
  • Ontology
  • Exceptions
  • Abstract Classes

Indices and tables

• Index

• Module Index

• Search Page