brad-enrichment 0.1.0

A command-line tool for BRAD enrichment analysis

Gene Enrichment with BRAD

1. note to self: openpyxl is an additional requirement beyond BRAD-DEV

Setup

Follow the below instructions to install the necessary dependencies and build the RAG database. This must be run one time when installing the system, and note that the dependencies identical to that of the BRAD repository with the addition of scrapetube and youtube_transcript_api.

Install Dependencies

Install BRAD This code must be run from the video-rag branch from the BRAD repository, and the roots of both repository must be located within the same directory. Run the below commands to install both repositories:

git clone https://github.com/Jpickard1/BRAD.git
git clone https://github.com/Jpickard1/BRAD-Video.git

Backend (python)

1. Activate BRAD-DEV or BRAD-1 conda environment used for developing the BRAD according to the specifications of that repository.

If you wish to expand the library of searchable videos beyond those provided, install the following dependencies:

2. pip install scrapetube
3. pip install youtube_transcript_api

Frontend (javascript) Run the following set of commands from the root of this repository.

curl -o- https://raw.githubusercontent.com/creationix/nvm/master/install.sh | bash
source ~/.nvm/nvm.sh
nvm install 20.18.0
nvm use 20.18.0
npm install --prefix ./brad-chat

Turn On

In separate terminals, execute the following commands from the root of this repository:

cd brad-chat
npm start

export OPENAI_API_KEY=<PLACE YOUR OPENAI API KEY HERE>
flask --app app run --host=0.0.0.0 --port=5000

Note Slight variations may be required if you are running this on windows or other systems.

Build New Video RAG Databases from Youtube (optional)

To build the RAG database:

python youtube_database_construction.py

Modifications

1. specify the youtube channel
2. specify the videos (we should add a new argument for this)

Cite As

@article{pickard2024language,
  title={Language Model Powered Digital Biology with BRAD},
  author={Pickard, Joshua and Prakash, Ram and Choi, Marc Andrew and Oliven, Natalie and
          Stansbury, Cooper and Cwycyshyn, Jillian
          and Gorodetsky, Alex and Velasquez, Alvaro and Rajapakse, Indika},
  journal={arXiv preprint arXiv:2409.02864},
  url={https://arxiv.org/abs/2409.02864},
  year={2024}
}