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TESTS Talk2AIAgents4Pharma Talk2BioModels Talk2KnowledgeGraphs TESTS Talk2Scholars Talk2Cells

Talk2AIAgents4Pharma Pulls Talk2BioModels Pulls Talk2KnowledgeGraphs Pulls Talk2Scholars Pulls

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)

AIAgents4Pharma

News

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

Watch the presentation

Getting Started

Installation

Option 1: Docker (stable-release)

We now have all the agents available on Docker Hub.

Choose your agent below for detailed Docker instructions:

Option 2: git (for developers and contributors)

Python Version from PEP 621 TOML

  1. Clone the repository:
git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma && cd AIAgents4Pharma
  1. 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
  1. 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
  1. 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

If your machine has NVIDIA GPU(s), please install the following this:

  • nvidia-cuda-toolkit
  • nvidia-container-toolkit (required for GPU support with Docker; enables containers to access NVIDIA GPUs for accelerated computing). After installing nvidia-container-toolkit, please restart Docker to ensure GPU support is enabled.

To use the Agents, you need a free NVIDIA API key. Create an account and apply for free credits here.

Talk2Scholars and Talk2KnowledgeGraphs requires Milvus to be set up as the vector database — install Milvus depending on your setup by following the official instructions for CPU or GPU. You will also need a Zotero API key, which you can generate here. (The Zotero key is only required for Talk2Scholars; all other agents do not need it.)

By default, talk2knowledgegraphs includes a small subset of the PrimeKG knowledge graph, allowing users to start interacting with it out of the box. To switch to a different knowledge graph or use your own, refer to the deployment guide. 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.

Option 3: pip (beta-release)

Python Version from PEP 621 TOML

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
  1. Make your changes and commit them:
git commit -m "feat: add a brief description of your change"
  1. Push your branch:
git push origin feat/your-feature-name
  1. 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

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