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

Please use version 1.26.2 or later for better support with NVIDIA NIM models.

Option 1: PyPI

pip install aiagents4pharma

Check out the tutorials on each agent for detailed instructions.

Option 2: Docker Hub

We now have Talk2AIAgents4Pharma, Talk2Biomodels, and Talk2Scholars available on Docker Hub.

Run Talk2AIAgents4Pharma and Talk2KnowledgeGraphs

Talk2AIAgents4Pharma and Talk2KnowledgeGraphs require Ollama for embedding models, so Docker Compose is used to run both containers in the same network.

Setup Environment Variables

1. Choose the app you want to use:

# Navigate to the correct directory before setting up environment variables.
# Use one of the following commands based on the agent you want to use:
cd AIAgents4Pharma/aiagents4pharma/talk2aiagents4pharma
cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs

1. Copy the .env.example file and rename it to .env:
   sh cp .env.example .env
2. Open the .env file and add your API keys:

plaintext OPENAI_API_KEY=your_openai_api_key NVIDIA_API_KEY=your_nvidia_api_key OLLAMA_HOST=http://ollama:11434 LANGCHAIN_TRACING_V2=true LANGCHAIN_API_KEY=your_langchain_api_key_here # Notes: # The API endpoint for Ollama is already set in env.example. # Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma. # If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed. # Langsmith API for tracing is optional for both, set it in env.example if required.

1. Save the file.

To start the containers, run the following command:

docker compose --profile cpu up # for CPU mode
docker compose --profile nvidia up # for GPU mode
docker compose --profile amd up # for AMD mode

This will:

• Pull the latest images if they are not already available.
• Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network.
• Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs.

To Access the web app, open your browser and go to:

http://localhost:8501

To stop the containers, run:

docker compose down

Run Talk2Biomodels and Talk2Scholars

1. Run the containers

bash 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

bash 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

1. 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:
  bash 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:
   bash git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma cd AIAgents4Pharma
2. Install dependencies:

bash 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

⚠️ pcst_fast 1.0.10 library requires Microsoft Visual C++ 14.0 or greater to be installed.
You can download Microsoft C++ Build Tools from here.

1. Initialize OPENAI_API_KEY and NVIDIA_API_KEY

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

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

1. Initialize ZOTERO_API_KEY and ZOTERO_USER_ID

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

Please note that ZOTERO keys are requried only if you want to launch Talk2Scholars. For all the other agents, please ignore this step.

1. [Optional] Initialize LANGSMITH_API_KEY

bash 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.

1. Launch the app:
   bash streamlit run app/frontend/streamlit_app_<agent>.py
   Replace <agent> with the agent name you are interested to launch.</agent>

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

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.

Feedback

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