cobra-component-models

SQLAlchemy ORM and pydantic data models for SQL storage and JSON serialization of COBRA components such as reactions, compounds, and compartments.


Keywords
cobra, orm, pydantic, serialization, sqlalchemy
License
Apache-2.0
Install
pip install cobra-component-models==0.5.0

Documentation

COBRA Component Models

Current PyPI Version Supported Python Versions Apache Software License Version 2.0 Code of Conduct Travis CI Codecov Black Documentation Status

Provide SQLAlchemy ORM and pydantic data models for SQL storage and serialization of COBRA components such as reactions, compounds, and compartments. They are loosely modeled after corresponding classes from the SBML Level 3 Version 2 specification. The data models are primarily intended for web services but other applications may benefit from these, too.

Install

It's as simple as:

pip install cobra-component-models

Usage

For now please take a look at the various class definitions and test cases to understand how to use the provided models.

Copyright

  • Copyright © 2019, Moritz E. Beber.
  • Copyright © 2018-2019, Institute for Molecular Systems Biology, ETH Zurich.
  • Copyright © 2018-2019, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.
  • Free software distributed under the Apache Software License 2.0.
  • Parts of the included codebase are licensed under the MIT license.