aiagents4pharma 1.25.1

AI Agents for drug discovery, drug development, and other pharmaceutical R&D.

Introduction

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 the following agents:

• Talk2BioModels (v1 released; v2 in progress): Engage directly with mathematical models in systems biology.
• Talk2KnowledgeGraphs (v1 in progress): Access and explore complex biological knowledge graphs for insightful data connections.
• Talk2Scholars (v1 in progress): Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
• Talk2Cells (v1 in progress): Query and analyze sequencing data with ease.
• Talk2AIAgents4Pharma (v1 in progress): Converse with all the agents above (currently supports T2B and T2KG)

Getting Started

Installation

Option 1: PyPI

pip install aiagents4pharma

Check out the tutorials on each agent for detailed instrcutions.

Option 2: Docker Hub

Both Talk2Biomodels and Talk2Scholars are now available on Docker Hub.

1. Pull the Docker images

   docker pull virtualpatientengine/talk2biomodels
   

   docker pull virtualpatientengine/talk2scholars
   

2. Run the containers

   docker run -d \
     --name talk2biomodels \
     -e OPENAI_API_KEY=<your_openai_api_key> \
     -e NVIDIA_API_KEY=<your_nvidia_api_key> \
     -p 8501:8501 \
     virtualpatientengine/talk2biomodels
   

   docker run -d \
     --name talk2scholars \
     -e OPENAI_API_KEY=<your_openai_api_key> \
     -e ZOTERO_API_KEY=<your_zotero_api_key> \
     -e ZOTERO_USER_ID=<your_zotero_user_id> \
     -p 8501:8501 \
     virtualpatientengine/talk2scholars
   

3. Access the Web App Open your browser and go to:

   http://localhost:8501
   

   You can create a free account at NVIDIA and apply for their free credits here.

Notes

• Ensure you replace <your_openai_api_key>, <your_nvidia_api_key>, <your_zotero_api_key>, and <your_zotero_user_id> with your actual credentials.
• Both applications use port 8501, so run them on different ports if needed:

  docker run -d -e OPENAI_API_KEY=<your_openai_api_key> -p 8501:8501 virtualpatientengine/talk2scholars
  

  Then, access it via http://localhost:8501.

Option 3: git

1. Clone the repository:

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

2. Install dependencies:

   pip install -r requirements.txt
   

   The current version of T2KG requires additional Ollama library to be installed.

   Ollama can be easily downloaded and installed from the following link: https://ollama.com/download

   As an alternative, use the following commands to install the library using terminal and to pull necessary model:

   • Ubuntu:

     curl -fsSL https://ollama.com/install.sh | sh
     ollama pull nomic-embed-text
     

   • Windows:

     curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip
     tar -xzf .\ollama-windows-amd64.zip
     start ollama serve
     ollama pull nomic-embed-text
     

   • macOS:

     brew install ollama
     ollama pull nomic-embed-text
     

   A list of pulled Ollama models can be checked using the following command:

   ollama list
   

3. Initialize OPENAI_API_KEY and NVIDIA_API_KEY

   export OPENAI_API_KEY=....
   export NVIDIA_API_KEY=....
   

   You can create a free account at NVIDIA and apply for their free credits here.

4. Initialize ZOTERO_API_KEY and ZOTERO_USER_ID

   export ZOTERO_API_KEY=....
   export ZOTERO_USER_ID=....
   

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 T2X-xxxx, where X can be AA4P (Main Agent), B (Biomodels), S (Scholars), KG (KnowledgeGraphs), or C (Cells). If you skip the previous step, it will default to the name default. xxxx will be the 4-digit ID created for the session.

6. Launch the app:

   streamlit run app/frontend/streamlit_app_<agent>.py
   

   Replace with the agent name you are interested to launch.

For detailed instructions on each agent, please refer to their respective modules.

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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 and reach out to any one of us below via Discussions:

   Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!

• Talk2Biomodels/Talk2Cells: @gurdeep330 @lilijap @dmccloskey
• Talk2KnowledgeGraphs: @awmulyadi @dmccloskey
• Talk2Scholars: @ansh-info @gurdeep330 @dmccloskey

Current Needs

• Beta testers for Talk2BioModels and Talk2Scholars.
• Developers with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.

Feel free to reach out to us via Discussions.

Check out our CONTRIBUTING.md for more information.

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Feedback

Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use Isssues or Discussions 😀