aiagents4pharma 1.36.0

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)

News

• T2B and T2KG accepted at the MLGenX workshop during ICLR #2025 in Singapore. Read More

Watch the presentation:

Getting Started

Installation

Option 1: Docker (stable-release)

We now have all the agents available on Docker Hub.

To run Talk2AIAgents4Pharma / Talk2KnowledgeGraphs

Both agents require Ollama to run embedding models like nomic-embed-text. We use a single startup script that automatically detects your hardware (NVIDIA, AMD, or CPU) and handles container startup, model loading, and service orchestration.

1. Clone the repository and navigate to the agent directory

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

cd AIAgents4Pharma/aiagents4pharma/<agent>

Replace <agent> with either:

• talk2aiagents4pharma
• talk2knowledgegraphs

2. Setup environment variables

Copy and configure your .env file:

cp .env.example .env

Then edit .env and add your API keys:

OPENAI_API_KEY=...                  # Required for both agents
NVIDIA_API_KEY=...                  # Required for both agents
OLLAMA_HOST=http://ollama:11434     # Required for AA4P / T2KG
LANGCHAIN_TRACING_V2=true           # Optional for both agents
LANGCHAIN_API_KEY=...               # Optional for both agents

To use Talk2AIAgents4Pharma or Talk2KnowledgeGraphs, you need a free NVIDIA API key. Create an account and apply for free credits here.

Notes for Windows Users

If you are using Windows, it is recommended to install Git Bash for a smoother experience when running the bash commands in this guide.

• For applications that use Docker Compose, Git Bash is required.
• For applications that use docker run manually, Git Bash is optional, but recommended for consistency.

You can download Git Bash here: Git for Windows.

When using Docker on Windows, make sure you run Docker with administrative privileges if you face permission issues.

To resolve for permission issues, you can:

• Review the official Docker documentation on Windows permission requirements.
• Alternatively, follow the community discussion and solutions on Docker Community Forums.

LangSmith support is optional. To enable it, create an API key here.

3. Start the application

Run the startup script. It will:

• Detect your hardware configuration (NVIDIA GPU, AMD GPU, or CPU). Apple Metal is unavailable inside Docker, and Intel SIMD optimizations are automatically handled without special configuration.
• Choose the correct Ollama image (latest or rocm)
• Launch the Ollama container with appropriate runtime settings
• Pull the required embedding model (nomic-embed-text)
• Start the agent after the model is available

chmod +x startup.sh
./startup.sh        # Add --cpu flag to force CPU mode if needed

4. Access the Web UI

Once started, the agent is available at:

http://localhost:8501

To Run Talk2Biomodels / Talk2Scholars

1. Run the containers

Talk2Biomodels

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

Talk2Scholars

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> \
  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
  -p 8501:8501 \
  virtualpatientengine/talk2scholars

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

   http://localhost:8501
   

To use Talk2BioModels or Talk2Scholars, you need a free NVIDIA API key. Create an account and apply for free credits here.

Only for Talk2Scholars, you also need a Zotero API key, which you can generate here. (For all other agents, the Zotero key is not required.)

If you are using docker on Windows, please follow these Windows Setup Notes.

LangSmith support is optional. To enable it, create an API key here.

Notes

• Be sure to replace the placeholder values with your actual credentials before running any container:

  • <your_openai_api_key>
  • <your_nvidia_api_key>
  • <your_zotero_api_key>
  • <your_zotero_user_id>

• All agents default to port 8501. If you plan to run multiple agents simultaneously, make sure to assign different ports to avoid conflicts.

  Example (Talk2Scholars on port 8502):

  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> \
    -e NVIDIA_API_KEY=<your_nvidia_api_key> \
    -p 8502:8501 \
    virtualpatientengine/talk2scholars
  

  Then access the app at: http://localhost:8502

Option 2: git (for developers and contributors)

1. Clone the repository:

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

2. Install dependencies:

We use Conda as our environment manager, Follow the official Quickstart install instructions provided by anaconda/miniconda.

conda create --name AIAgents4Pharma python=3.12 -y && conda activate AIAgents4Pharma && pip install --upgrade pip && pip install -r requirements.txt

3. Initialize API Keys

   export OPENAI_API_KEY=....          # Required for all agents
   export NVIDIA_API_KEY=....          # Required for all agents
   export ZOTERO_API_KEY=....          # Required for T2S
   export ZOTERO_USER_ID=....          # Required for T2S
   export LANGCHAIN_TRACING_V2=true    # Optional for all agents
   export LANGCHAIN_API_KEY=...        # Optional for all agents
   

To use Talk2AIAgents4Pharma, Talk2BioModels, Talk2KnowledgeGraphs, or Talk2Scholars, you need a free NVIDIA API key. Create an account and apply for free credits here.

Only for Talk2Scholars, you also need a Zotero API key, which you can generate here. (For all other agents, the Zotero key is not required.)

To use Talk2Scholars, you must have FAISS installed through Conda. Follow installation instructions for your OS here.

To use Talk2AIAgents4Pharma or Talk2KnowledgeGraphs, you must have Ollama installed. Follow installation instructions for your OS here.

After installing, pull the nomic-embed-text model and start the server by running:

ollama pull nomic-embed-text && ollama serve

More details about the model are available here.

Additionally on Windows, the pcst_fast 1.0.10 library requires Microsoft Visual C++ 14.0 or greater.
You can download the Microsoft C++ Build Tools here.

LangSmith support is optional. To enable it, create an API key here.

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.

4. Launch the app:

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

   Replace <agent> with the agent name you are interested to launch:

• talk2aiagents4pharma
• talk2biomodels
• talk2knowledgegraphs
• talk2scholars
• talk2cells

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

Option 3: pip (beta-release)

pip install aiagents4pharma

Check out the tutorials on each agent for detailed instructions.

Contributing

We welcome your support to make AIAgents4Pharma even better.
All types of contributions are appreciated — whether you're fixing bugs, adding features, improving documentation, or helping with testing, every contribution is valuable.

How to contribute

1. Star this repository to show your support.
2. Fork the repository.
3. Create a new branch for your work:

   git checkout -b feat/your-feature-name
   

4. Make your changes and commit them:

   git commit -m "feat: add a brief description of your change"
   

5. Push your branch:

   git push origin feat/your-feature-name
   

6. Open a Pull Request.

Areas where you can help

• Beta testing for Talk2BioModels and Talk2Scholars.
• Development work related to Python, bioinformatics, or knowledge graphs.

Contacts for contributions

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

Please refer to our CONTRIBUTING.md for more detailed contribution guidelines.

Feedback

If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.
Please open an issue or start a discussion