AnyBio: Bioinformatics Research AI Assistant

AnyBio is a Streamlit-based application that allows users to interact with a bioinformatics knowledge base. It uses Google Generative AI and FAISS for document embedding and retrieval.

Prerequisites

Before running the application, ensure you have the following installed:

1. Python 3.8 or higher: Download Python
2. pip: Python's package manager (comes with Python installation).
3. Virtual Environment (optional): Recommended to isolate dependencies.

Setup Instructions

1. Clone the Repository

Clone the repository to your local machine:

git clone <repository-url>
cd AnyBio

2. Create a Virtual Environment (Optional but Recommended)

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install Dependencies

Install the required Python packages:

pip install -r requirements.txt

4. Configure Environment Variables

Create a .env file in the root directory and add the following:

GOOGLE_API_KEY=<your-google-api-key>

Replace <your-google-api-key> with your actual Google AI API key.

5. Add PDF Files

Place the PDF files you want to process in the data directory. Create the directory if it does not exist:

mkdir data

6. Run the Application

Start the Streamlit app:

streamlit run app.py

7. Access the Application

Open your browser and navigate to:

http://localhost:8501

Features

• Multi-language Support: Supports English, Spanish, Amharic, and Arabic.
• PDF Processing: Extracts and indexes text from PDF files.
• Knowledge Base Management: Recreate or clear the FAISS vector store.
• Chat Interface: Ask bioinformatics-related questions and get responses based on the knowledge base.

Troubleshooting

• Missing API Key: Ensure the .env file contains a valid Google API key.
• PDF Directory Not Found: Create the data directory and add PDF files.
• Dependencies Issue: Ensure all dependencies are installed using pip install -r requirements.txt.

License

This project is licensed under the MIT License. See the LICENSE file for details.