A performant reimplementation of the UniRep protein featurization model in JAX.
The UniRep model was developed in George Church's lab, see the original publication here (bioRxiv) or here (Nature Methods), as well as the repository containing the original model.
This repo is a self-contained and easily customizable version of the UniRep model, with additional utility APIs that support protein engineering workflows.
Ensure that your compute environment allows you to run JAX code. (A modern Linux or macOS with a GLIBC>=2.23 is probably necessary.)
Then, you can install from PyPI:
pip install jax-unirep
If you want the latest and greatest, you can install directly from source:
pip install git+https://github.com/ElArkk/jax-unirep.git
Documentation on how to use jax-unirep is available here.
We highly encourage community contributions to this project! For more information, see the section in the docs on our contributing guidelines.
To read more about how we reimplemented the model in JAX, check out our preprint on bioarxiv.
All the model weights are licensed under the terms of Creative Commons Attribution-NonCommercial 4.0 International License. To view a copy of this license, visit here) or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
Otherwise the code in this repository is licensed under the terms of GPL v3.
FAQs
A performant and user-friendly reimplementation of UniRep in JAX.
We found that jax-unirep demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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