BRAD: Bioinformatics Digital Assistant

Please see the projects main page available here!

Docker

The Docker build can be used to deploy brad without having to install packages manually. after installing either docker desktop or docker engine docker intsallation, you can run the following commands to install and run BRAD

To build the dockerfile:

docker build -t brad:local .

With docker compose:

cd deployment
docker compose up -d

OR with just docker

docker run -e OPENAI_API_KEY=your_open_ai_key -e  PYDANTIC_SKIP_VALIDATING_CORE_SCHEMAS='True' -p 5001:5000 -p 3000:3000  brad:full_frontend

then proceed to http://localhost:3000

Development

Documentation

To build the projects documentation in the ReadTheDocs html formatting, in the docs/ directory, run the command make html. This will populate the docs/build/html directory with the webpages. The docs/build/ directory is excluded from git but will automatically be built when pushing to main.

During the build, the tutorials/ directory is automatically pulled in to the source by copying all jupyter notebooks. These are included in the user guide section of the documentation.

To remove the documentation from docs/build/ run make clean from the same directory where you built it.

Cite Us

@article{pickard2024bioinformatics,
  title={Language Model Powered Digital Biology},
  author={Pickard, Joshua and Choi, Marc Andrew and Oliven, Natalie and
          Stansbury, Cooper and Cwycyshyn, Jillian and Galioto, Nicholas
          and Gorodetsky, Alex and Velasquez, Alvaro and Rajapakse, Indika},
  journal={arXiv preprint arXiv:2409.02864},
  url={https://arxiv.org/abs/2409.02864},
  year={2024}
}