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🤖 AIAgents4Pharma

Welcome to AIAgents4Pharma – an open-source project by Team VPE that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.

Our toolkit currently consists of three agents, each designed to simplify and enhance access to complex data in biology:

  • Talk2BioModels: Engage directly with mathematical models in systems biology.

  • Talk2Cells (Work in progress): Query and analyze sequencing data with ease.

  • Talk2KnowledgeGraphs (Coming soon): Access and explore complex biological knowledge graphs for insightful data connections.

Prerequisites

  • Python 3.10+
  • Git
  • Required libraries specified in requirements.txt

Installation

Option 1: PyPI

pip install aiagents4pharma

Check out the tutorials on each agent for detailed instrcutions.

Option 2: Git

  1. Clone the repository:

    git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
    cd AIAgents4Pharma
    

  2. Install dependencies:

    pip install -r requirements.txt
    

  3. Initialize OPENAI_API_KEY

    export OPENAI_API_KEY = ....
    

  4. [Optional] Set up login credentials

    vi .streamlit/secrets.toml
    
    and enter
    password='XXX'
    
    Please note that the passowrd will be same for all.

  5. [Optional] Initialize LANGSMITH_API_KEY

    export LANGCHAIN_TRACING_V2=true
    export LANGCHAIN_API_KEY=<your-api-key>
    
    Please note that this will create a new tracing project in your Langsmith account with the name <user_name>@<uuid>, where user_name is the name you provided in the previous step. If you skip the previous step, it will default to default (a 128 bit unique ID created for the session).

  6. Launch the app:

    streamlit run app/frontend/streamlit_app.py
    

Contributing

We welcome contributions to AIAgents4Pharma! Here’s how you can help:

  1. Fork the repository
  2. Create a new branch for your feature (git checkout -b feat/feature-name)
  3. Commit your changes (git commit -m 'feat: Add new feature')
  4. Push to the branch (git push origin feat/feature-name)
  5. Open a pull request

Check out our CONTRIBUTING.md for more information.