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| title: 🤖 VCell BioModel Chatbot | |
| emoji: 🧬 | |
| colorFrom: blue | |
| colorTo: purple | |
| sdk: streamlit | |
| sdk_version: 1.44.1 | |
| app_file: app.py | |
| pinned: true | |
| license: mit | |
| short_description: Demo Chatbot to query VCell modeling resources | |
| <h1 align="center">VCell BioModel Chatbot Demo</h1> | |
| <p align="center"> | |
| <img src="misc/gsoc.png" alt="Google Summer of Code Logo" width="100"/> | |
| <img src="misc/NRNB.png" alt="NRNB Logo" width="200"/> | |
| <br><br> | |
| <a href="https://share.streamlit.io/KacemMathlouthi/VCell-Demo"> | |
| <img src="https://static.streamlit.io/badges/streamlit_badge_black_white.svg" alt="View in Streamlit" /> | |
| </a> | |
| </p> | |
| This demo presents an intelligent chatbot interface for querying and interpreting biomodels stored in the [VCell BioModel Database](https://vcell.cam.uchc.edu/api/v0/biomodel). It enables users to interact with biological modeling resources using natural language and provides structured outputs, model metadata, downloadable files, and visualizations in real time. This work was developed as a demo for the NRNB Organization for **Google Summer of Code 2025**. | |
| <p align="center"> | |
| <img src="https://i.imgur.com/FgayjY9.png" alt="GSoC VCell Demo" width = "600" /> | |
| </p> | |
| --- | |
| ## Overview | |
| This chatbot is an AI-powered assistant capable of: | |
| - Interpreting natural language queries | |
| - Extracting structured parameters | |
| - Querying the VCell API | |
| - Summarizing model data in a human-readable way using a large language model (LLM) | |
| - Visualizing model diagrams | |
| - Providing downloadable model files | |
| --- | |
| ## Features | |
| - **Natural Language Interface** — Query the database with simple English prompts | |
| - **LLM Parameters Extraction** — Uses LLaMA 3 to extract structured parameters | |
| - **VCell API Integration** — Supports dynamic querying with filters like author, category, biomodelid... | |
| - **Summarization** — Generates high-level descriptions of model contents in a human | |
| [gif of parameters extraction, API response and summarization] | |
| - **Visualization** — Displays system reaction diagrams from the API | |
| - **Download Options** — Direct links to SBML and VCML formats for downstream use | |
| [gif of downloading the provided files and visualizations] | |
| - **Streamlit UI** — Minimalist, responsive, and easy to deploy | |
| --- | |
| ## Technologies Used | |
| - Python | |
| - Streamlit | |
| - Groq API for the LLM (LLaMA 3.3-70B) | |
| - VCell Public API | |
| - Pydantic (parameter schema) | |
| - Dotenv (secret management) | |
| --- | |
| ## Getting Started | |
| ### Prerequisites | |
| - Python 3.10 or higher | |
| - A valid Groq API key | |
| ### Installation | |
| ```bash | |
| git clone https://github.com/KacemMathlouthi/VCell-Demo.git | |
| cd VCell-Demo | |
| python -m venv .venv | |
| source .venv/bin/activate | |
| pip install -r requirements.txt | |
| ``` | |
| ### Configuration | |
| Create a `.env` file at the root of the project: | |
| ```env | |
| LLM_API_KEY=your_groq_api_key_here | |
| ``` | |
| ### Run the Application | |
| ```bash | |
| streamlit run app.py | |
| ``` | |
| Visit `http://localhost:8501` to start using the chatbot. | |
| --- | |
| ## Example Prompts | |
| Here are some questions the chatbot can understand: | |
| - `List all public models by user ion` | |
| - `Find the model with ID 201844485` | |
| - `Show VCell models related to calcium` | |
| --- | |
| ## Project Structure | |
| ``` | |
| ├── app.py # Main application entry point | |
| ├── requirements.txt # Project dependencies | |
| ├── .env # Environment variable for API key | |
| ├── .streamlit/config.toml # UI configuration | |
| ├── vcelldb/ | |
| │ ├── vcell_api.py # Wrapper for VCell API calls | |
| │ ├── diagram.py # Utilities for diagrams and downloads | |
| │ └── params_model.py # Schema definitions | |
| └── utils/ | |
| ├── llm_helper.py # LLM instance creation and response generation | |
| └── params_extraction.py # Prompt-to-parameter process | |
| ``` | |
| --- | |
| ## License | |
| This project is licensed under the [MIT License](LICENSE). You are free to use, modify, and distribute the software with proper attribution. | |
| Special thanks to the **Virtual Cell (VCell)** team and the **National Resource for Network Biology (NRNB)** for their support. | |
| For more information, visit [vcell.org](https://vcell.org). |