/trill-app

This repository contains a Streamlit app that provides a user-friendly interface for TRILL (TRaining and Inference using the Language of Life), a sandbox for creative protein engineering and discovery.

Primary LanguagePythonMIT LicenseMIT

markdown

TRILL Protein Engineering Streamlit App

Summary

This repository contains a Streamlit app that provides a user-friendly interface for TRILL (TRaining and Inference using the Language of Life), a sandbox for creative protein engineering and discovery. This app allows researchers to perform various operations related to protein engineering using pretrained models and user-provided input files.

Features

  • Upload protein sequences in FASTA, PDB, or CIF formats
  • Run various TRILL operations, such as embedding, fine-tuning, generating, folding, and visualizing
  • Customize TRILL run configurations, such as the number of GPUs, RNG seed, and model type
  • Extend the app to support more command-line arguments and features

Usage

To use this app, first install the dependencies and then run the Streamlit app using the following command:

$ streamlit run trill_app.py

The app should open in your default web browser, allowing you to interact with the TRILL program.

Requirements

  • Python 3.8 or later
  • Streamlit
  • TRILL-Proteins
  • PyG-Lib and related dependencies

Installation

  1. Clone this repository:
$ git clone https://github.com/your_username/trill-streamlit-app.git
  1. Change into the trill-streamlit-app directory:
$ cd trill-streamlit-app
  1. Install the dependencies:
$ conda create -n trill_env python=3.10
$ conda activate trill_env
$ pip install streamlit
$ pip install trill-proteins
$ pip install pyg-lib torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.13.0+cu117.html
  1. Run the app:
$ streamlit run trill_app.py

Contributing

If you'd like to contribute to this project, please follow these steps:

  1. Fork the repository
  2. Create a new branch for your feature or bugfix (git checkout -b my-feature-branch)
  3. Make changes and commit them to your branch
  4. Push your changes to your forked repository (git push origin my-feature-branch)
  5. Create a new Pull Request for your changes

Authors

License

This project is licensed under the MIT License - see the LICENSE.md file for details